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Frossard V, Sabatier P, Bruel R, Vagnon C, Tissot N, Curt-Grand-Gaudin N, Perga ME. Intense touristic activities exceed climate change to shape aquatic communities in a mountain lake. AQUATIC SCIENCES 2023; 85:71. [PMID: 37192889 PMCID: PMC10157129 DOI: 10.1007/s00027-023-00968-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/10/2023] [Indexed: 05/18/2023]
Abstract
Mountain lakes are especially vulnerable to climate change, but are also increasingly exposed to local anthropogenic development through winter and summer tourism. In this study, we aimed to tease apart the influence of tourism from that of climate in a mountain lake located within one of the largest French ski resorts, by combining paleolimnological and present ecological data. The reconstructed long-term ecological dynamics highlighted an increase in lake biological production from the end of the Little Ice Age up to the 1950s, suggesting a historical dominance of climate control. Afterward, a major drop in pelagic production occurred at the same time as the watershed erosion increased and peaked in the 1990s, concomitant with massive digging for the ski resort expansion. The benthic invertebrates collapsed in the 1980s, concomitantly with the onset of massive salmonid stocking and recent warming. Stable isotope analyses identified benthic invertebrates as the major salmonid diet resource and suggested a possible direct impact of salmonid stocking on benthic invertebrates. However, habitat use may differ among salmonid species as suggested by the way fish DNA was preserved in surficial sediment. The high abundances of macrozooplankton further confirmed the limited reliance of salmonids on pelagic resources. The variable thermal tolerance of benthic invertebrates suggested that the recent warming may mostly affect littoral habitats. Our results indicate that winter and summer tourism may differently affect the biodiversity of mountain lakes and could collectively interfere with the ecological impacts of recent warming, making local management of primary importance to preserve their ecological integrity. Supplementary Information The online version contains supplementary material available at 10.1007/s00027-023-00968-6.
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Affiliation(s)
- Victor Frossard
- UMR42 CARRTEL Université Savoie Mont Blanc, INRAE, Thonon-les-Bains, France
| | - Pierre Sabatier
- UMR 5204 EDYTEM, Université Savoie Mont Blanc, CNRS, 73376 Le Bourget du lac, France
| | - Rosalie Bruel
- UMR42 CARRTEL Université Savoie Mont Blanc, INRAE, Thonon-les-Bains, France
- OFB, Pôle ECLA, Aix-en-Provence, France
| | - Chloé Vagnon
- UMR42 CARRTEL Université Savoie Mont Blanc, INRAE, Thonon-les-Bains, France
| | - Nathalie Tissot
- UMR42 CARRTEL Université Savoie Mont Blanc, INRAE, Thonon-les-Bains, France
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, France
| | | | - Marie-Elodie Perga
- Faculty of Geosciences and Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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Nickel J, Cordellier M. Cost-saving population genomic investigation of Daphnia longispina complex resting eggs using whole-genome amplification and pre-sequencing screening. Ecol Evol 2022; 12:e9682. [PMID: 36582775 PMCID: PMC9793289 DOI: 10.1002/ece3.9682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/02/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Resting stages of aquatic organisms that accumulate in the sediment over time are an exceptional resource that allows direct insights into past populations and addressing evolutionary questions. This is of particular interest in taxa that face relatively new environmental challenges, e.g., climate change and eutrophication, such as the Daphnia longispina species complex, a keystone zooplankton group in European freshwater ecosystems. However, genomic analysis might be challenging as DNA yield from many of these resting stages can be low and the material degraded. To reliably allow the resequencing of single Daphnia resting eggs from different sediment layers and characterize genomic changes through time, we performed whole-genome amplification to obtain DNA amounts suitable for genome resequencing and tested multiple protocols involving egg isolation, whole-genome amplification kits, and library preparation. A pre-sequencing contamination screening was developed, consisting of amplifying mitochondrial Daphnia and bacterial markers, to quickly assess and exclude possibly contaminated samples. In total, we successfully amplified and sequenced nine genomes from Daphnia resting eggs that could be identified as Daphnia longispina species. We analyzed the genome coverage and heterozygosity of these samples to optimize this method for future projects involving population genomic investigation of the resting egg bank.
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Affiliation(s)
- Jana Nickel
- Institute of Animal Cell and Systems BiologyUniversity of HamburgHamburgGermany
| | - Mathilde Cordellier
- Institute of Animal Cell and Systems BiologyUniversity of HamburgHamburgGermany
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Tsugeki N, Nakane K, Doi H, Ochi N, Kuwae M. Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA. Sci Rep 2022; 12:1741. [PMID: 35110566 PMCID: PMC8810866 DOI: 10.1038/s41598-021-03899-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/10/2021] [Indexed: 11/09/2022] Open
Abstract
Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.
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Affiliation(s)
- Narumi Tsugeki
- Faculty of Law, Matsuyama University, Matsuyama, 790-8578, Ehime, Japan.
| | - Kai Nakane
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, 650-0047, Hyogo, Japan
| | - Natsuki Ochi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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Reversed evolution of grazer resistance to cyanobacteria. Nat Commun 2021; 12:1945. [PMID: 33782425 PMCID: PMC8007715 DOI: 10.1038/s41467-021-22226-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
Exploring the capability of organisms to cope with human-caused environmental change is crucial for assessing the risk of extinction and biodiversity loss. We study the consequences of changing nutrient pollution for the freshwater keystone grazer, Daphnia, in a large lake with a well-documented history of eutrophication and oligotrophication. Experiments using decades-old genotypes resurrected from the sediment egg bank revealed that nutrient enrichment in the middle of the 20th century, resulting in the proliferation of harmful cyanobacteria, led to the rapid evolution of grazer resistance to cyanobacteria. We show here that the subsequent reduction in nutrient input, accompanied by a decrease in cyanobacteria, resulted in the re-emergence of highly susceptible Daphnia genotypes. Expression and subsequent loss of grazer resistance occurred at high evolutionary rates, suggesting opposing selection and that maintaining resistance was costly. We provide a rare example of reversed evolution of a fitness-relevant trait in response to relaxed selection. Anthropogenic changes, such as eutrophication from lake pollution, can lead to rapid evolution. Comparing Daphnia resurrected from generations adapted to historical pollution to contemporary, post-cleanup populations finds that Daphnia rapidly reversed their evolved resistance to harmful cyanobacteria.
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Cornetti L, Fields PD, Van Damme K, Ebert D. A fossil-calibrated phylogenomic analysis of Daphnia and the Daphniidae. Mol Phylogenet Evol 2019; 137:250-262. [DOI: 10.1016/j.ympev.2019.05.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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Grabenstein KC, Taylor SA. Breaking Barriers: Causes, Consequences, and Experimental Utility of Human-Mediated Hybridization. Trends Ecol Evol 2018; 33:198-212. [DOI: 10.1016/j.tree.2017.12.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
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Thielsch A, Knell A, Mohammadyari A, Petrusek A, Schwenk K. Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evol Biol 2017; 17:227. [PMID: 29166859 PMCID: PMC5700674 DOI: 10.1186/s12862-017-1070-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. RESULTS We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). CONCLUSIONS A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.
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Affiliation(s)
- Anne Thielsch
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany.
| | - Alexis Knell
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
| | - Ali Mohammadyari
- Faculty of Science, Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Adam Petrusek
- Faculty of Science, Department of Ecology, Charles University, Prague, Czechia
| | - Klaus Schwenk
- Institute for Environmental Sciences, Molecular Ecology, University of Koblenz-Landau, Landau in der Pfalz, Germany
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10
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Liu P, Xu L, Xu SL, Martínez A, Chen H, Cheng D, Dumont HJ, Han BP, Fontaneto D. Species and hybrids in the genus Diaphanosoma Fischer, 1850 (Crustacea: Branchiopoda: Cladocera). Mol Phylogenet Evol 2017; 118:369-378. [PMID: 29107154 DOI: 10.1016/j.ympev.2017.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 01/22/2023]
Abstract
Cladocerans are well-studied planktonic crustaceans, especially those of the genus Daphnia in which interesting evolutionary questions have been addressed on speciation processes. The aim of the present study is to demonstrate that other genera of cladocerans show similar levels of cryptic diversity, intraspecific gene flow, and thus become useful model systems for comparison. In order to do so, we chose the genus Diaphanosoma, widespread in tropical and temperate areas. We started with a survey of species diversity in the genus Diaphanosoma in Asia using a morphological approach, then obtained sequences from a mitochondrial and a nuclear marker from multiple individuals of different species, performed tests on DNA taxonomy and molecular phylogenies, and assessed the role of hybridization in explaining the cases of mitonuclear discordance. The results are that cryptic diversity occurs in Diaphanosoma, and mitonuclear discordance was found in about 6% of the sequenced animals. Past hybridization is supported as the most likely explanation for the discordance: no evidence was found of first generation hybrids with heterozygous sequences. Our analysis on patterns of genetic diversity in Diaphanosoma supports similarities and differences with what is known in Daphnia.
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Affiliation(s)
- Ping Liu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Lei Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shao-Lin Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Alejandro Martínez
- National Research Council of Italy, Institute of Ecosystem Study, Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | - Hua Chen
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Dan Cheng
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Henri J Dumont
- Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bo-Ping Han
- Jinan University, Department of Ecology, Guangzhou 510632, China.
| | - Diego Fontaneto
- National Research Council of Italy, Institute of Ecosystem Study, Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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