1
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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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2
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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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3
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O'Grady CJ, Dhandapani V, Colbourne JK, Frisch D. Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs. Mol Ecol Resour 2021; 22:946-961. [PMID: 34672105 DOI: 10.1111/1755-0998.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.
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Affiliation(s)
- Christopher James O'Grady
- School of Life Sciences, University of Warwick, Coventry, UK.,Cell and Gene Therapy Catapult, London, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Dagmar Frisch
- School of Biosciences, University of Birmingham, Birmingham, UK.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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4
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Cordellier M, Wojewodzic MW, Wessels M, Kuster C, von Elert E. Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment. ZOOLOGY 2021; 145:125895. [PMID: 33561655 DOI: 10.1016/j.zool.2021.125895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/25/2023]
Abstract
Hatching resting stages of ecologically important organisms such as Daphnia from lake sediments, referred to as resurrection ecology, is a powerful approach to assess changes in alleles and traits over time. However, the utility of the approach is constrained by a few obstacles, including low and/or biased hatching among genotypes. Here, we eliminated such bottlenecks by investigating DNA sequences isolated directly (i.e. without hatching) from resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. While we expected genome-wide changes, we specifically expected changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise FST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances. In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.
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Affiliation(s)
- Mathilde Cordellier
- Universität Hamburg, Biozentrum Grindel, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
| | - Marcin W Wojewodzic
- Cancer Registry of Norway (Kreftregisteret), Institute of Population-Based Cancer Research, Etiology Group, NO-0304, Oslo, Norway; School of Biosciences, University of Birmingham, B15 2TT, United Kingdom.
| | - Martin Wessels
- Institute for Lake Research at the Agency for Environment Baden-Württemberg, 88085, Langenargen, Germany.
| | - Christian Kuster
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
| | - Eric von Elert
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
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5
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Dane M, Anderson NJ, Osburn CL, Colbourne JK, Frisch D. Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability. Ecol Evol 2020; 10:14178-14188. [PMID: 33391708 PMCID: PMC7771157 DOI: 10.1002/ece3.7012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Climate and environmental condition drive biodiversity at many levels of biological organization, from populations to ecosystems. Combined with paleoecological reconstructions, palaeogenetic information on resident populations provides novel insights into evolutionary trajectories and genetic diversity driven by environmental variability. While temporal observations of changing genetic structure are often made of sexual populations, little is known about how environmental change affects the long-term fate of asexual lineages. Here, we provide information on obligately asexual, triploid Daphnia populations from three Arctic lakes in West Greenland through the past 200-300 years to test the impact of environmental change on the temporal and spatial population genetic structure. The contrasting ecological state of the lakes, specifically regarding salinity and habitat structure may explain the observed lake-specific clonal composition over time. Palaeolimnological reconstructions show considerable regional environmental fluctuations since 1,700 (the end of the Little Ice Age), but the population genetic structure in two lakes was almost unchanged with at most two clones per time period. Their local populations were strongly dominated by a single clone that has persisted for 250-300 years. We discuss possible explanations for the apparent population genetic stability: (a) persistent clones are general-purpose genotypes that thrive under broad environmental conditions, (b) clonal lineages evolved subtle genotypic differences unresolved by microsatellite markers, or (c) epigenetic modifications allow for clonal adaptation to changing environmental conditions. Our results motivate research into the mechanisms of adaptation in these populations, as well as their evolutionary fate in the light of accelerating climate change in the polar regions.
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Affiliation(s)
- Maison Dane
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | | | - Christopher L. Osburn
- Department of Marine, Earth, and Atmospheric SciencesNorth Carolina State UniversityRaleighNCUSA
| | | | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
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6
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Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 2020; 3:169. [PMID: 32265485 PMCID: PMC7138834 DOI: 10.1038/s42003-020-0899-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
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7
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Giguet-Covex C, Ficetola GF, Walsh K, Poulenard J, Bajard M, Fouinat L, Sabatier P, Gielly L, Messager E, Develle AL, David F, Taberlet P, Brisset E, Guiter F, Sinet R, Arnaud F. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Sci Rep 2019; 9:14676. [PMID: 31604959 PMCID: PMC6789010 DOI: 10.1038/s41598-019-50339-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/12/2019] [Indexed: 11/09/2022] Open
Abstract
Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).
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Affiliation(s)
- C Giguet-Covex
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK. .,EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France.
| | - G F Ficetola
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.,Department of Environmental Science and Policy, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - K Walsh
- BioArch-Department of Archaeology, University of York, York, YO10 5DD, UK
| | - J Poulenard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - M Bajard
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Fouinat
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - P Sabatier
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - L Gielly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Messager
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - A L Develle
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
| | - F David
- CEREGE, UMR CNRS 7330, IRD 161-Marseille Université, Technopôle de l'Arbois Méditerranée, BP 80, 13545, Aix en Provence cedex 4, France
| | - P Taberlet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - E Brisset
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - F Guiter
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - R Sinet
- Aix-Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Aix-en-Provence, France
| | - F Arnaud
- EDYTEM, UMR 5204 CNRS, Univ. Savoie Mont Blanc, Pôle Montagne, 73376, Le Bourget du Lac, France
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8
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García-Roger EM, Lubzens E, Fontaneto D, Serra M. Facing Adversity: Dormant Embryos in Rotifers. THE BIOLOGICAL BULLETIN 2019; 237:119-144. [PMID: 31714860 DOI: 10.1086/705701] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An in-depth look at the basic aspects of dormancy in cyclic parthenogenetic organisms is now possible thanks to research efforts conducted over the past two decades with rotifer dormant embryos. In this review, we assemble and compose the current knowledge on four central themes: (1) distribution of dormancy in animals, with an overview on the phylogenetic distribution of embryo dormancy in metazoans, and (2) physiological and cellular processes involved in dormancy, with a strong emphasis on the dormant embryos of cyclically parthenogenetic monogonont rotifers; and discussions of (3) the selective pressures and (4) the evolutionary and population implications of dormancy in these animals. Dormancy in metazoans is a widespread phenomenon with taxon-specific features, and rotifers are among the animals in which dormancy is an intrinsic feature of their life cycle. Our review shows that embryo dormancy in rotifers shares common functional pathways with other taxa at the molecular and cellular level, despite the independent evolution of dormancy across phyla. These pathways include the arrest of similar metabolic routes and the usage of common metabolites for the stabilization of cellular structures and to confer stress resistance. We conclude that specific features of recurrent harsh environmental conditions are a powerful selective pressure for the fine-tuning of dormancy patterns in rotifers. We hypothesize that similar mechanisms at the organism level will lead to similar adaptive consequences at the population level across taxa, among which the formation of egg banks, the coexistence of species, and the possibility of differentiation among populations and local adaptation stand out. Our review shows how studies of rotifers have contributed to improved knowledge of all of these aspects.
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9
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Siegenthaler A, Wangensteen OS, Soto AZ, Benvenuto C, Corrigan L, Mariani S. Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Mol Ecol Resour 2018; 19:206-220. [PMID: 30358106 PMCID: PMC7379652 DOI: 10.1111/1755-0998.12956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/30/2022]
Abstract
Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high‐throughput DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large‐scale, routine estuarine biodiversity monitoring.
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Affiliation(s)
- Andjin Siegenthaler
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Ana Z Soto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Chiara Benvenuto
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Laura Corrigan
- Environment Agency, Tyneside House, Newcastle upon Tyne, UK
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
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10
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Summers JL, Bernik B, Saunders CJ, McLachlan JS, Blum MJ. A century of genetic variation inferred from a persistent soil-stored seed bank. Evol Appl 2018; 11:1715-1731. [PMID: 30344638 PMCID: PMC6183470 DOI: 10.1111/eva.12675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 12/31/2022] Open
Abstract
Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil-stored seed banks as natural archives, in part because of concerns over nonrandom attrition and mixed stratification. Here, we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records of demographic and population genetic variation. After assembling profiles of the seed bank from radionuclide-dated soil cores, we germinated seeds to "resurrect" cohorts spanning the 20th century. Using microsatellite markers, we assessed genetic diversity and differentiation among depth cohorts, drawing comparisons to extant plants at the study site and in nearby and more distant marshes. We found that seed density peaked at intermediate soil depths. We also detected genotypic differences among cohorts as well as between cohorts and extant plants. Genetic diversity did not decline with depth, indicating that the observed pattern of differentiation is not due to attrition. Patterns of differentiation within and among extant marshes also suggest that local populations persist as aggregates of small clones, likely reflecting repeated seedling recruitment and low immigration from admixed regional gene pools. These findings indicate that persistent and stratified soil-stored seed banks merit further consideration as resources for reconstructing decadal- to century-long records that can lend insight into the tempo and nature of ecological and evolutionary processes that shape populations over time.
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Affiliation(s)
- Jennifer L. Summers
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana
| | - Brittany Bernik
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana
| | - Colin J. Saunders
- Southeast Environmental Research CenterFlorida International UniversityMiamiFlorida
| | - Jason S. McLachlan
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
| | - Michael J. Blum
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana
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11
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Lack JB, Weider LJ, Jeyasingh PD. Whole genome amplification and sequencing of a
Daphnia
resting egg. Mol Ecol Resour 2017; 18:118-127. [DOI: 10.1111/1755-0998.12720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/10/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Justin B. Lack
- CCR Collaborative Bioinformatics Resource National Cancer Institute NIH Bethesda MD USA
- Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. Frederick MD USA
| | - Lawrence J. Weider
- Department of Biology Program in Ecology & Evolutionary Biology University of Oklahoma Norman OK USA
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12
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Korosi JB, Thienpont JR, Smol JP, Blais JM. Paleo-ecotoxicology: What Can Lake Sediments Tell Us about Ecosystem Responses to Environmental Pollutants? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9446-9457. [PMID: 28763202 DOI: 10.1021/acs.est.7b02375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The development of effective risk reduction strategies for aquatic pollutants requires a comprehensive understanding of toxic impacts on ecosystems. Classical toxicological studies are effective for characterizing pollutant impacts on biota in a controlled, simplified environment. Nonetheless, it is well-acknowledged that predictions based on the results of these studies must be tested over the long-term in a natural ecosystem setting to account for increased complexity and multiple stressors. Paleolimnology (the study of lake sediment cores to reconstruct environmental change) can address many key knowledge gaps. When used as part of a weight-of-evidence framework with more traditional approaches in ecotoxicology, it can facilitate rapid advances in our understanding of the chronic effects of pollutants on ecosystems in an environmentally realistic, multistressor context. Paleolimnology played a central role in the Acid Rain debates, as it was instrumental in demonstrating industrial emissions caused acidification of lakes and associated ecosystem-wide impacts. "Resurrection Ecology" (hatching dormant resting eggs deposited in the past) records evolutionary responses of populations to chronic pollutant exposure. With recent technological advances (e.g., geochemistry, genomic approaches), combined with an emerging paleo-ecotoxicological framework that leverages strengths across multiple disciplines, paleolimnology will continue to provide valuable insights into the most pressing questions in ecotoxicology.
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Affiliation(s)
- Jennifer B Korosi
- Department of Geography, York University , Toronto, Ontario Canada , M3J 1P3
| | - Joshua R Thienpont
- Department of Biology, University of Ottawa , Ottawa, Ontario Canada , K1N 6N5
| | - John P Smol
- Paleoecological Environmental Assessment and Research Lab (PEARL), Department of Biology, Queen's University , Kingston, Ontario Canada , K7L 3N6
| | - Jules M Blais
- Department of Biology, University of Ottawa , Ottawa, Ontario Canada , K1N 6N5
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13
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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Frisch D, Morton PK, Chowdhury PR, Culver BW, Colbourne JK, Weider LJ, Jeyasingh PD. A millennial-scale chronicle of evolutionary responses to cultural eutrophication inDaphnia. Ecol Lett 2014; 17:360-8. [DOI: 10.1111/ele.12237] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/16/2013] [Accepted: 11/26/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Dagmar Frisch
- University of Oklahoma; Biological Station; Kingston OK 73439 USA
| | - Philip K. Morton
- University of Oklahoma; Biological Station; Kingston OK 73439 USA
| | | | - Billy W. Culver
- University of Oklahoma; Biological Station; Kingston OK 73439 USA
- University of Oklahoma; Department of Biology; Norman OK 73071 USA
| | - John K. Colbourne
- University of Birmingham; School of Biosciences; Birmingham B15 2TT UK
| | - Lawrence J. Weider
- University of Oklahoma; Biological Station; Kingston OK 73439 USA
- University of Oklahoma; Department of Biology; Norman OK 73071 USA
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Hundred years of environmental change and phytoplankton ecophysiological variability archived in coastal sediments. PLoS One 2013; 8:e61184. [PMID: 23593424 PMCID: PMC3623915 DOI: 10.1371/journal.pone.0061184] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 03/07/2013] [Indexed: 11/30/2022] Open
Abstract
Marine protist species have been used for several decades as environmental indicators under the assumption that their ecological requirements have remained more or less stable through time. However, a growing body of evidence suggests that marine protists, including several phytoplankton species, are in fact highly diverse and may quickly respond to changes in the environment. Predicting how future climate will impact phytoplankton populations is important, but this task has been challenged by a lack of time-series of ecophysiological parameters at time-scales relevant for climate studies (i.e. at least decadal). Here, we report on ecophysiological variability in a marine dinoflagellate over a 100-year period of well-documented environmental change, by using the sedimentary archive of living cysts from a Scandinavian fjord (Koljö Fjord, Sweden). During the past century, Koljö Fjord has experienced important changes in salinity linked to the North Atlantic Oscillation (NAO). We revived resting cysts of Pentapharsodinium dalei preserved in the fjord sediments and determined growth rates for 18 strains obtained from 3 sediment core layers at salinity 15 and 30, which represent extreme sea-surface conditions during periods of predominantly negative and positive NAO phases, respectively. Upper pH tolerance limits for growth were also tested. In general, P. dalei grew at a higher rate in salinity 30 than 15 for all layers, but there were significant differences among strains. When accounting for inter-strain variability, cyst age had no effect on growth performance or upper pH tolerance limits for this species, indicating a stable growth response over the 100-year period in spite of environmental fluctuations. Our findings give some support for the use of morphospecies in environmental studies, particularly at decadal to century scales. Furthermore, the high intra-specific variability found down to sediment layers dated as ca. 50 years-old indicates that cyst-beds of P. dalei are repositories of ecophysiological diversity.
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Woodhams DC, Bosch J, Briggs CJ, Cashins S, Davis LR, Lauer A, Muths E, Puschendorf R, Schmidt BR, Sheafor B, Voyles J. Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis. Front Zool 2011; 8:8. [PMID: 21496358 PMCID: PMC3098159 DOI: 10.1186/1742-9994-8-8] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 04/18/2011] [Indexed: 12/29/2022] Open
Abstract
Background Rescuing amphibian diversity is an achievable conservation challenge. Disease mitigation is one essential component of population management. Here we assess existing disease mitigation strategies, some in early experimental stages, which focus on the globally emerging chytrid fungus Batrachochytrium dendrobatidis. We discuss the precedent for each strategy in systems ranging from agriculture to human medicine, and the outlook for each strategy in terms of research needs and long-term potential. Results We find that the effects of exposure to Batrachochytrium dendrobatidis occur on a spectrum from transient commensal to lethal pathogen. Management priorities are divided between (1) halting pathogen spread and developing survival assurance colonies, and (2) prophylactic or remedial disease treatment. Epidemiological models of chytridiomycosis suggest that mitigation strategies can control disease without eliminating the pathogen. Ecological ethics guide wildlife disease research, but several ethical questions remain for managing disease in the field. Conclusions Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.
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Affiliation(s)
- Douglas C Woodhams
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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Graham AL, Shuker DM, Pollitt LC, Auld SKJR, Wilson AJ, Little TJ. Fitness consequences of immune responses: strengthening the empirical framework for ecoimmunology. Funct Ecol 2010. [DOI: 10.1111/j.1365-2435.2010.01777.x] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, 08 544, USA
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
- Centre for Immunity, Infection, and Evolution; School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
| | | | - Laura C. Pollitt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
| | - Stuart K. J. R. Auld
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
| | - Alastair J. Wilson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
| | - Tom J. Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
- Centre for Immunity, Infection, and Evolution; School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
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McTaggart SJ, Conlon C, Colbourne JK, Blaxter ML, Little TJ. The components of the Daphnia pulex immune system as revealed by complete genome sequencing. BMC Genomics 2009; 10:175. [PMID: 19386092 PMCID: PMC2685406 DOI: 10.1186/1471-2164-10-175] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2008] [Accepted: 04/22/2009] [Indexed: 01/08/2023] Open
Abstract
Background Branchiopod crustaceans in the genus Daphnia are key model organisms for investigating interactions between genes and the environment. One major theme of research on Daphnia species has been the evolution of resistance to pathogens and parasites, but lack of knowledge of the Daphnia immune system has limited the study of immune responses. Here we provide a survey of the immune-related genome of D. pulex, derived from the newly completed genome sequence. Genes likely to be involved in innate immune responses were identified by comparison to homologues from other arthropods. For each candidate, the gene model was refined, and we conducted an analysis of sequence divergence from homologues from other taxa. Results and conclusion We found that some immune pathways, in particular the TOLL pathway, are fairly well conserved between insects and Daphnia, while other elements, in particular antimicrobial peptides, could not be recovered from the genome sequence. We also found considerable variation in gene family copy number when comparing Daphnia to insects and present phylogenetic analyses to shed light on the evolution of a range of conserved immune gene families.
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Affiliation(s)
- Seanna J McTaggart
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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20
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Martins N, Bollinger C, Harper RM, Ribeiro R. Effects of acid mine drainage on the genetic diversity and structure of a natural population of Daphnia longispina. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2009; 92:104-112. [PMID: 19230987 DOI: 10.1016/j.aquatox.2009.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 01/15/2009] [Accepted: 01/17/2009] [Indexed: 05/27/2023]
Abstract
The increase in resistance to contaminants can result in the loss of genetic diversity of impacted populations. In this work, the effects of acid mine drainage (AMD) on the genetic diversity and structure of a historically exposed population of Daphnia longispina were evaluated using amplified fragment length polymorphism (AFLP) analysis. Individual sensitivity to acute copper exposure was determined in order to characterize the populations in terms of metal tolerance and in an attempt to identify possible contaminant indicative bands (CIB). No reduction in genetic diversity was found in the AMD impacted site population, in comparison to two reference populations. However, the analysis of molecular variance indicated a significant genetic differentiation from the two reference populations and a significant correlation between individual genetic distance and tolerance. The different average tolerance of individuals presenting one specific AFLP band indicated the existence of one putative CIB.
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Affiliation(s)
- Nelson Martins
- IMAR-Instituto do Mar, Department of Zoology, University of Coimbra, Largo Marquês de Pombal, P-3004 517 Coimbra, Portugal. aa
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21
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The impact of human-made ecological changes on the genetic architecture of Daphnia species. Proc Natl Acad Sci U S A 2009; 106:4758-63. [PMID: 19273852 DOI: 10.1073/pnas.0807187106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The overenrichment (eutrophication) of aquatic ecosystems with nutrients leading to algal blooms and anoxic conditions has been a persistent and widespread environmental problem. Although there are many studies on the ecological impact of elevated phosphorus (P) levels (e.g., decrease in biodiversity and water quality), little is known about the evolutionary consequences for animal species. We reconstructed the genetic architecture of a Daphnia species complex in 2 European lakes using diapausing eggs that were isolated from sediment layers covering the past 100 years. Changes in total P were clearly associated with a shift in species composition and the population structure of evolutionary lineages. Although environmental conditions were largely re-established after peak eutrophication during the 1970s and 1980s, original species composition and the genetic architecture of species were not restored but evolved along new evolutionary trajectories. Our data demonstrate that anthropogenically induced temporal alterations of habitats are associated with long-lasting changes in communities and species via interspecific hybridization and introgression.
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Eads BD, Andrews J, Colbourne JK. Ecological genomics in Daphnia: stress responses and environmental sex determination. Heredity (Edinb) 2007; 100:184-90. [PMID: 17519967 DOI: 10.1038/sj.hdy.6800999] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Ecological genomics is the study of adaptation of natural populations to their environment, and therefore seeks to link organism and population level processes through an understanding of genome organization and function. The planktonic microcrustacean Daphnia, which has long been an important system for ecology, is now being used as a genomic model as well. Here we review recent progress in selected areas of Daphnia genomics research. Production of parthenogenetic male offspring occurs through environmental cues, which clearly involves endocrine regulation and has also been studied as a toxicological response to juvenoid hormone analog insecticides. Recent progress has uncovered a putative juvenoid cis-response element, which together with microarray analysis will stimulate further research into nuclear hormone receptors and their associated transcriptional regulatory networks. Ecotoxicological studies indicate that mRNA profiling is a sensitive and specific research tool with promising applications in environmental monitoring and for uncovering conserved cellular processes. Rapid progress is expected to continue in these and other areas, as genomic tools for Daphnia become widely available to investigators.
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Affiliation(s)
- B D Eads
- Center for Genomics and Bioinformatics, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405-3700, USA.
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Wyn B, Sweetman JN, Leavitt PR, Donald DB. Historical metal concentrations in lacustrine food webs revealed using fossil ephippia from Daphnia. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2007; 17:754-64. [PMID: 17494394 DOI: 10.1890/06-0868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Metal contamination of freshwater ecosystems is increasingly prevalent due to anthropogenic activities such as metal smelting and fossil fuel combustion. While toxicological studies focus on aqueous metal concentrations that result in lethal or sublethal responses, currently the only method for reconstructing a lake's metal contamination history is through an examination of the sedimentary deposits. In this paper, we suggest that cladoceran diapausing eggs (ephippia), which are abundant in nature and accumulate maternally derived metals, can be used to measure historical variations in biologically relevant metals that derive from the water column (water, diet). Linear regressions of total metal content against ephippia density or mass were strong (R2 > 0.80, P < 0.04) and revealed that metals were incorporated into ephippia with little contamination from the sediment matrix. Comparison of metal concentrations in ephippia and bulk sediments from three lakes demonstrated that some metals associated with urban sources (Cd, Cr, Mo) were preferentially concentrated in ephippia, whereas concentrations of other metals indicating landscape erosion (Al, Ca, Fe, Mn) exhibited greater concentrations in bulk sediments than in diapausing eggs. Because historical changes in metals within fossils and bulk sediments were uncorrelated in most instances, past variation in the metal content of ephippia provided a unique history of food web exposure to metals in the water column.
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Affiliation(s)
- B Wyn
- Limnology Laboratory, Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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Are they still viable? Physical conditions and abundance of Daphnia pulicaria resting eggs in sediment cores from lakes in the Tatra Mountains. Biologia (Bratisl) 2006. [DOI: 10.2478/s11756-006-0126-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Shepherd LD, Millar CD, Ballard G, Ainley DG, Wilson PR, Haynes GD, Baroni C, Lambert DM. Microevolution and mega-icebergs in the Antarctic. Proc Natl Acad Sci U S A 2005; 102:16717-22. [PMID: 16275908 PMCID: PMC1283793 DOI: 10.1073/pnas.0502281102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Indexed: 11/18/2022] Open
Abstract
Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.
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Affiliation(s)
- L D Shepherd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Albany, Auckland, New Zealand
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Ortells R, Reusch TBH, Lampert W. Salinity tolerance in Daphnia magna: characteristics of genotypes hatching from mixed sediments. Oecologia 2005; 143:509-16. [PMID: 15800749 DOI: 10.1007/s00442-005-0027-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 01/26/2005] [Indexed: 10/25/2022]
Abstract
The hatching of diapausing eggs is a means of temporal dispersal that can provide populations with genotypes adapted to different environments. In a salinity-variable shallow lake, we predicted that the mixing of different age-classes of eggs in the sediment may yield genotypes with different salinity optima. The alternative would be the absence of local adaptation and the presence of a homogenous population of salt-tolerant genotypes with high phenotypic plasticity. We tested these alternatives by isolating Daphnia magna resting eggs from different sediment depths, exposing them to hatching cues at different salinity levels and measuring the performance of hatched individuals. Results revealed a homogeneous sediment with generally broad-tolerance genotypes and some genotypes with low salt tolerance, which supports the second hypothesis. However, the disturbed character of the sediment hampered historical reconstruction. The absence of local adaptation in the diapausing egg bank may be the result of various scenarios in the response of D. magna populations to severe salinity changes in the lake.
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Affiliation(s)
- Raquel Ortells
- Department of Physiological Ecology, Max Planck Institute of Limnology, Postfach 165, Plon, 24302, Germany.
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COLBOURNE JK, ROBISON B, BOGART K, LYNCH M. Five hundred and twenty-eight microsatellite markers for ecological genomic investigations using Daphnia. ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00721.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hutchinson WF, van Oosterhout C, Rogers SI, Carvalho GR. Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proc Biol Sci 2003; 270:2125-32. [PMID: 14561275 PMCID: PMC1691486 DOI: 10.1098/rspb.2003.2493] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite increasing evidence that current exploitation rates can contribute to shifts in life-history traits and the collapse of marine fish stocks, few empirical studies have investigated the likely evolutionary impacts. Here, we used DNA recovered from a temporal series of archived North Sea cod (Gadus morhua) otoliths, to investigate genetic diversity within the Flamborough Head population between 1954 and 1998, during which time the population underwent two successive declines. Microsatellite data indicated a significant reduction in genetic diversity between 1954 and 1970 (total number of alleles: 1954, 46; 1960, 42; 1970, 37), and a subsequent recovery between 1970 and 1998 (total number of alleles: 1970, 37; 1981, 42; 1998, 45). Furthermore, estimates of genetic differentiation (F(ST) and R(ST)) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change. Other studies indicate that diversity at neutral microsatellite loci may be correlated with variability at selected genes, thus compromising a population's subsequent recovery and adaptive potential. Such effects are especially pertinent to North Sea cod, which are threatened by continuing exploitation and rising sea temperatures.
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Affiliation(s)
- William F Hutchinson
- Molecular Ecology and Fisheries Genetics Laboratory, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK.
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