1
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Lynch M, Wei W, Ye Z, Pfrender M. The genome-wide signature of short-term temporal selection. Proc Natl Acad Sci U S A 2024; 121:e2307107121. [PMID: 38959040 PMCID: PMC11252749 DOI: 10.1073/pnas.2307107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Despite evolutionary biology's obsession with natural selection, few studies have evaluated multigenerational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a 10-y population-genomic survey of the microcrustacean Daphnia pulex. The genome sequences of [Formula: see text]800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the following: the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals); the preponderance of weak positive selection operating on minor alleles; and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that interannual fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the further development of theoretical expressions for the interpretation of population-genomic data.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ85287
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ85287
| | - Zhiqiang Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan430079, China
| | - Michael Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
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2
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Spear MM, Levi SJ, Etterson JR, Gross BL. Resurrecting urban sunflowers: Phenotypic and molecular changes between antecedent and modern populations separated by 36 years. Mol Ecol 2023; 32:5241-5259. [PMID: 37667619 DOI: 10.1111/mec.17112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/31/2023] [Indexed: 09/06/2023]
Abstract
Resurrection experiments provide a unique opportunity to evaluate phenotypic and molecular evolution in response to environmental challenges. To understand the evolution of urban populations of Helianthus annuus, we compared plants from 36-year-old antecedent seed collections to modern seed collections from the same area using molecular and quantitative genetic approaches. We found 200 differentially expressed transcripts between antecedent and modern groups, and transcript expression was generally higher in modern samples as compared to antecedent samples. Admixture analysis indicated gene flow from domesticated to modern populations over time. After a greenhouse refresher generation, one antecedent-modern population pair was grown under two water availability (well-watered and drought) and temperature (ambient and elevated by 2.8°C) conditions reflecting historical and contemporary climates. Overall, 78% (7 out of 9) of traits differed between the antecedent and modern populations, with modern individuals displaying some trait changes that are coherent with climate changes expectations and some trait changes in the direction of crop varieties. Phenotypic selection analysis showed that modern trait values were often favoured by selection, especially in environmental treatments resembling modern conditions. Trait heritability in the antecedent population was five times as high as in the modern population, on average. In addition, phenotypic plasticity for some traits, such as flowering phenology, was present in the antecedent population but absent in the modern population. The combination of phenotypic and molecular information suggests that evolution has been influenced by crop-wild introgression, adaptive processes and drift. We discuss these results in the context of continued evolution in response to anthropogenic factors.
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Affiliation(s)
- Marissa M Spear
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Sophie J Levi
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Julie R Etterson
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
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3
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El-Sabaawi RW, Lemmen KD, Jeyasingh PD, Declerck SAJ. SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics. Ecol Lett 2023; 26 Suppl 1:S109-S126. [PMID: 37840025 DOI: 10.1111/ele.14285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 10/17/2023]
Abstract
Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics.
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Affiliation(s)
- Rana W El-Sabaawi
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Kimberley D Lemmen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Steven A J Declerck
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KULeuven, Leuven, Belgium
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4
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Lynch M, Wei W, Ye Z, Pfrender M. The Genome-wide Signature of Short-term Temporal Selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538790. [PMID: 37162919 PMCID: PMC10168312 DOI: 10.1101/2023.04.28.538790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Despite evolutionary biology's obsession with natural selection, few studies have evaluated multi-generational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a nine-year population-genomic survey of the microcrustacean Daphnia pulex. The genome-sequences of > 800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals), the preponderance of weak negative selection operating on minor alleles, and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the development of new theoretical expressions for the interpretation of population-genomic data.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
| | - Michael Pfrender
- Department of Biological Sciences, Notre Dame University, Notre Dame, IN 46556
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5
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Jones CLC, Shafer ABA, Frost PC. Characterizing nutritional phenotypes using experimental nutrigenomics: Is there nutrient-specificity to different types of dietary stress? Mol Ecol 2023; 32:1073-1086. [PMID: 36528862 DOI: 10.1111/mec.16825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The ability to directly measure and monitor poor nutrition in individual animals and ecological communities is hampered by methodological limitations. In this study, we use nutrigenomics to identify nutritional biomarkers in a freshwater zooplankter, Daphnia pulex, a ubiquitous primary consumer in lakes and a sentinel of environmental change. We grew animals in six ecologically relevant nutritional treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium and high Cyanobacteria. We extracted RNA for transcriptome sequencing to identify genes that were nutrient responsive and capable of predicting nutritional status with a high degree of accuracy. We selected a list of 125 candidate genes, which were subsequently pruned to 13 predictive potential biomarkers. Using a nearest-neighbour classification algorithm, we demonstrate that these potential biomarkers are capable of classifying our samples into the correct nutritional group with 100% accuracy. The functional annotation of the selected biomarkers revealed some specific nutritional pathways and supported our hypothesis that animal responses to poor nutrition are nutrient specific and not simply different presentations of slow growth or energy limitation. This is a key step in uncovering the causes and consequences of nutritional limitation in animal consumers and their responses to small- and large-scale changes in biogeochemical cycles.
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Affiliation(s)
- Catriona L C Jones
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada.,Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - Paul C Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
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6
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Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One 2022; 17:e0265103. [PMID: 35834446 PMCID: PMC9282536 DOI: 10.1371/journal.pone.0265103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Hamanda B. Cavalheri
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Thiago G. Lima
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Natalie T. Jones
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Daniela Zarate
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Eric Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan B. Shurin
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
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7
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Wagner ND, Simmons DBD, Prater C, Frost PC. Proteome changes in an aquatic invertebrate consumer in response to different nutritional stressors. Oecologia 2022; 199:329-341. [PMID: 35661252 DOI: 10.1007/s00442-022-05198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/21/2022] [Indexed: 11/26/2022]
Abstract
Nutrient imbalances in zooplankton are caused by the differences in elemental content of producers and the demand for elements in consumers, which alter the life-history traits in consumers. Changes in life-history traits are mediated through metabolic pathways that affect gene expression and the metabolome. However, less is known about proteomic changes to elemental-limitation in zooplankton. Here, we grew Daphnia pulex under high food quantity and quality (HF), low food quantity (LF), and phosphorus (P)-limited (PL) diets for six days and measured growth, elemental composition, and the proteome. Daphnids in both LF and PL diets grew less. Animals in LF diets had less carbon (C), while daphnids in PL diets had less P compared to HF fed animals. In total, we identified 1719 proteins that were used in a partial least squares regression discriminant analysis (PLS-DA). Focusing on a subset of the proteome, the PLS-DA resulted in a clear separation between animals fed HF diets and PL and LF diets. Many proteome changes in nutrient-limited diets are associated with growth, reproduction, lipid metabolism, and nutrient assimilation. Regardless of the limiting nutrient, there were less hemoglobin and small subunit processome component proteins compared to HF fed animals. Daphnids fed LF diets had less vitellogenin fused superoxide dismutase and more lipid-droplet hydrolase, whereas Daphnia fed PL diets had higher abundances of cytochrome P450 and serine protease. Our proteome results compliment other "omic" studies that could be used to study Daphnia physiology in lakes.
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Affiliation(s)
- Nicole D Wagner
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, Texas, USA.
| | | | - Clay Prater
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Paul C Frost
- Department of Biology, Tent University, Peterborough, ON, Canada
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8
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Barnard-Kubow KB, Becker D, Murray CS, Porter R, Gutierrez G, Erickson P, Nunez JCB, Voss E, Suryamohan K, Ratan A, Beckerman A, Bergland AO. Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex. Mol Biol Evol 2022; 39:msac121. [PMID: 35642301 PMCID: PMC9198359 DOI: 10.1093/molbev/msac121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.
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Affiliation(s)
- Karen B Barnard-Kubow
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
- Department of Biology, University of Marburg, Marburg, Germany
| | - Connor S Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Robert Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Grace Gutierrez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Erin Voss
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Andrew Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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9
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Xu Z, Li Y, Li M, Liu H. Transcriptomic response of Daphnia magna to nitrogen- or phosphorus-limited diet. Ecol Evol 2021; 11:11009-11019. [PMID: 34429898 PMCID: PMC8366849 DOI: 10.1002/ece3.7889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Effects of nutrient-imbalanced diet on the growth and fitness of zooplankton were widely reported as key issues to aquatic ecology. However, little is known about the molecular mechanisms driving the physiological changes of zooplankton under nutrient stress.In this study, we investigated the physiological fitness and transcriptomic response of Daphnia magna when exposed to nitrogen (N)-limited or phosphorus (P)-limited algal diet (Chlamydomonas reinhardtii) compared to regular algae (N and P saturated).D. magna showed higher ingestion rates and overexpression of genes encoding digestive enzymes when fed with either N-limited or P-limited algae, reflecting the compensatory feeding. Under P-limitation, both growth rate and reproduction rate of D. magna were greatly reduced, which could be attributed to the downregulated genes within the pathways of cell cycle and DNA replication. Growth rate of D. magna under N-limitation was similar to normal group, which could be explained by the high methylation level (by degradation of methionine) supporting the body development.Phenotypic changes of D. magna under nutrient stress were explained by gene and pathway regulations from transcriptome data. Generally, D. magna invested more on growth under N-limitation but kept maintenance (e.g., cell structure and defense to external stress) in priority under P-limitation. Post-translational modifications (e.g., methylation and protein folding) were important for D. magna to deal with nutrient constrains.This study reveals the fundamental mechanisms of zooplankton in dealing with elemental imbalanced diet and sheds light on the transfer of energy and nutrient in aquatic ecosystems.
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Affiliation(s)
- Zhimeng Xu
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen UniversityShenzhenChina
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyKowloonChina
- Shenzhen Key Laboratory of Marine Microbiome EngineeringInstitute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Yingdong Li
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyKowloonChina
| | - Meng Li
- SZU‐HKUST Joint PhD Program in Marine Environmental ScienceShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome EngineeringInstitute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Hongbin Liu
- Department of Ocean ScienceThe Hong Kong University of Science and TechnologyKowloonChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong LaboratoryThe Hong Kong University of Science and TechnologyHong KongChina
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10
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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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11
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Jeyasingh PD, Goos JM, Lind PR, Roy Chowdhury P, Sherman RE. Phosphorus supply shifts the quotas of multiple elements in algae and
Daphnia
: ionomic basis of stoichiometric constraints. Ecol Lett 2020; 23:1064-1072. [DOI: 10.1111/ele.13505] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/20/2020] [Accepted: 03/11/2020] [Indexed: 12/22/2022]
Affiliation(s)
| | - Jared M. Goos
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- BioFire Diagnostics Salt Lake City UT USA
| | - Patrick R. Lind
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Priyanka Roy Chowdhury
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Department of Biology Keene State College Keene NH USA
| | - Ryan E. Sherman
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
- Biology Program MacMurray College Jacksonville IL USA
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12
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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: 27] [Impact Index Per Article: 6.8] [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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13
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Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer. Mol Biol Evol 2019; 37:475-487. [DOI: 10.1093/molbev/msz234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Knowledge of the molecular basis of phenotypic responses to environmental cues is key to understanding the process of adaptation. Insights to adaptation at an evolutionary time scale can be gained by observing organismal responses before and after a shift in environmental conditions, but such observations can rarely be made. Using the ecological and genomic model Daphnia, we linked transcriptomic responses and phosphorus (P)-related phenotypic traits under high and low P availability. We mapped weighted gene coexpression networks to traits previously assessed in resurrected ancient (600 years old) and modern Daphnia pulicaria from a lake with a historic shift in P-enrichment. Subsequently, we assessed evolutionary conservation or divergence in transcriptional networks of the same isolates. We discovered highly preserved gene networks shared between ancient genotypes and their modern descendants, but also detected clear evidence of transcriptional divergence between these evolutionarily separated genotypes. Our study highlights that phenotypic evolution is a result of molecular fine-tuning on different layers ranging from basic cellular responses to higher order phenotypes. In a broader context, these findings advance our understanding how populations are able to persist throughout major environmental shifts.
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14
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Peñuelas J, Fernández‐Martínez M, Ciais P, Jou D, Piao S, Obersteiner M, Vicca S, Janssens IA, Sardans J. The bioelements, the elementome, and the biogeochemical niche. Ecology 2019; 100:e02652. [DOI: 10.1002/ecy.2652] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/26/2018] [Accepted: 01/16/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Josep Peñuelas
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra 08193 Spain
- CREAF Cerdanyola del Valles 08193 Spain
| | - Marcos Fernández‐Martínez
- CREAF Cerdanyola del Valles 08193 Spain
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l'Environnement IPSL Gif‐sur‐Yvette 91191 France
| | - David Jou
- Department of Physics Universitat Autònoma de Barcelona Bellaterra 08193 Spain
| | - Shilong Piao
- Sino‐French Institute for Earth System Science College of Urban and Environmental Sciences Peking University Beijing 100871 China
| | - Michael Obersteiner
- International Institute for Applied Systems Analysis (IIASA), Ecosystems Services and Management Schlossplatz 1 Laxenburg A‐2361 Austria
| | - Sara Vicca
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems (PLECO) Department of Biology University of Antwerp Wilrijk B‐2610 Belgium
| | - Jordi Sardans
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra 08193 Spain
- CREAF Cerdanyola del Valles 08193 Spain
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15
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Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
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Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
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16
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Yousey AM, Chowdhury PR, Biddinger N, Shaw JH, Jeyasingh PD, Weider LJ. Resurrected 'ancient' Daphnia genotypes show reduced thermal stress tolerance compared to modern descendants. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172193. [PMID: 29657812 PMCID: PMC5882736 DOI: 10.1098/rsos.172193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/16/2018] [Indexed: 05/25/2023]
Abstract
Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest. We hypothesized clones were adapted to the thermal regimes of their respective time periods. We performed two thermal shock experiments that varied in length of heat exposure. Overall trends revealed that younger genotypes exhibited higher thermal tolerance than older genotypes; heat shock protein (hsp70) expression increased with temperature and varied among genotypes, but not across time periods. Our results indicate temperature may have been a selective factor on this population, although the observed responses may be a function of multifarious selection. Prior work found striking changes in population genetic structure, and in other traits that were strongly correlated with anthropogenic changes. Resurrection ecology approaches should help our understanding of interactive effects of anthropogenic alterations to temperature and other stressors on the evolutionary fate of natural populations.
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Affiliation(s)
- Aime'e M. Yousey
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Priyanka Roy Chowdhury
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Nicole Biddinger
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Punidan D. Jeyasingh
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA
| | - Lawrence J. Weider
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
- Program in Ecology and Evolutionary Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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17
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Burge DRL, Edlund MB, Frisch D. Paleolimnology and resurrection ecology: The future of reconstructing the past. Evol Appl 2018; 11:42-59. [PMID: 29302271 PMCID: PMC5748527 DOI: 10.1111/eva.12556] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
Paleolimnologists have utilized lake sediment records to understand historical lake and landscape development, timing and magnitude of environmental change at lake, watershed, regional and global scales, and as historical datasets to target watershed and lake management. Resurrection ecologists have long recognized lake sediments as sources of viable propagules ("seed or egg banks") with which to explore questions of community ecology, ecological response, and evolutionary ecology. Most researchers consider Daphnia as the primary model organism in these efforts, but many other aquatic biota, from viruses to macrophytes, similarly produce viable propagules that are incorporated in the sediment record but have been underutilized in resurrection ecology. The common goals shared by these two disciplines have led to mutualistic and synergistic collaborations-a development that must be encouraged to expand. We give an overview of the achievements of paleolimnology and the reconstruction of environmental history of lakes, review the untapped diversity of aquatic organisms that produce dormant propagules, compare Daphnia as a model of resurrection ecology with other organisms amenable to resurrection studies, especially diatoms, and consider new research directions that represent the nexus of these two fields.
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Affiliation(s)
- David R. L. Burge
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
- Water Resources Science Graduate ProgramUniversity of MinnesotaSt. PaulMNUSA
| | - Mark B. Edlund
- St. Croix Watershed Research StationScience Museum of MinnesotaMarine on St. CroixMNUSA
| | - Dagmar Frisch
- School of BiosciencesUniversity of BirminghamBirminghamUK
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18
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Sherman RE, Chowdhury PR, Baker KD, Weider LJ, Jeyasingh PD. Genotype-specific relationships among phosphorus use, growth and abundance in Daphnia pulicaria. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170770. [PMID: 29308224 PMCID: PMC5749992 DOI: 10.1098/rsos.170770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply.
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Affiliation(s)
- Ryan E. Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Kristina D. Baker
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lawrence J. Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK, USA
| | - Punidan D. Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
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19
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Simpson AM, Jeyasingh PD, Belden JB. Assessment of biochemical mechanisms of tolerance to chlorpyrifos in ancient and contemporary Daphnia pulicaria genotypes. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 193:122-127. [PMID: 29059598 DOI: 10.1016/j.aquatox.2017.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
The evolution of tolerance to environmental contaminants in non-target taxa has been largely studied by comparing extant populations experiencing contrasting exposure. Previous research has demonstrated that "resurrected" genotypes from a population of Daphnia pulicaria express temporal variation in sensitivity to the insecticide chlorpyrifos. Ancient genotypes (1301-1646AD.) were on average more sensitive to this chemical compared to the contemporary genotypes (1967-1977AD.). To determine the physiological mechanisms of tolerance, a series of biochemical assays was performed on three ancient and three contemporary genotypes; these six genotypes exhibited the most sensitive and most tolerant phenotypes within the population, respectively. Metabolic tolerance mechanisms were evaluated using acute toxicity testing, while target-site tolerance was assessed via in vitro acetylcholinesterase (AChE) assays. Acute toxicity tests were conducted using i) the toxic metabolite chlorpyrifos-oxon (CPF-oxon) and ii) CPF-oxon co-applied with piperonyl butoxide (PBO), a known Phase-I metabolic inhibitor. Both series of toxicity tests reduced the mean variation in sensitivity between tolerant and sensitive genotypes. Exposure to CPF-O reduced the disparity from a 4.7-fold to 1.6-fold difference in sensitivity. The addition of PBO further reduced the variation to a 1.2-fold difference in sensitivity. In vitro acetylcholinesterase assays yielded no significant differences in constitutive activity or target-site sensitivity. These findings suggest that pathways involving Phase-I detoxification and/or bioactivation of chlorpyrifos play a significant role in dictating the microevolutionary trajectories of tolerance in this population.
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Affiliation(s)
- Adam M Simpson
- Oklahoma State University, Stillwater, OK 74078, United States; Penn State Erie, The Behrend College, Erie, PA 16563, United States.
| | | | - Jason B Belden
- Oklahoma State University, Stillwater, OK 74078, United States
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20
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Weider LJ, Jeyasingh PD, Frisch D. Evolutionary aspects of resurrection ecology: Progress, scope, and applications-An overview. Evol Appl 2017; 11:3-10. [PMID: 29302267 PMCID: PMC5748524 DOI: 10.1111/eva.12563] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023] Open
Abstract
This perspective provides an overview to the Special Issue on Resurrection Ecology (RE). It summarizes the contributions to this Special Issue, and provides background information and future prospects for the use of RE in both basic and applied evolutionary studies.
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Affiliation(s)
- Lawrence J Weider
- Department of Biology Program in Ecology and Evolutionary Biology University of Oklahoma Norman OK USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology Oklahoma State University Stillwater OK USA
| | - Dagmar Frisch
- School of Biosciences University of Birmingham Birmingham UK
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21
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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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22
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Hales NR, Schield DR, Andrew AL, Card DC, Walsh MR, Castoe TA. Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia. Mol Ecol 2017. [PMID: 28628257 DOI: 10.1111/mec.14213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., "within-generation phenotypic plasticity") as well as induce heritable phenotypic responses that persist for multiple generations (i.e., "transgenerational plasticity", TGP). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within- and TGP at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within- and across generations using a clone of Daphnia ambigua that is known to exhibit strong TGP but weak within-generation plasticity. Daphnia were reared in the presence of predator cues in generation 1, and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes, but such shifts were 3-4× larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first-generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programmes involved in within- vs. transgeneration plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.
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Affiliation(s)
- Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Audra L Andrew
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew R Walsh
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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23
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Turner CB, Wade BD, Meyer JR, Sommerfeld BA, Lenski RE. Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170497. [PMID: 28791173 PMCID: PMC5541568 DOI: 10.1098/rsos.170497] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/21/2017] [Indexed: 05/25/2023]
Abstract
Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50 000 generations. The bacteria evolved higher relative nitrogen and phosphorus content, consistent with selection for increased use of the more abundant elements. Total carbon assimilated also increased, indicating more efficient use of the limiting element. We also measured stoichiometry in one population repeatedly through time. Stoichiometry changed more rapidly in early generations than later on, similar to the trajectory seen for competitive fitness. Altogether, our study shows that stoichiometry evolved over long time periods, and that it did so in a predictable direction, given the carbon-limited environment.
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Affiliation(s)
- Caroline B. Turner
- Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian D. Wade
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Justin R. Meyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Brooke A. Sommerfeld
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Richard E. Lenski
- Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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24
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Frisch D, Morton PK, Culver BW, Edlund MB, Jeyasingh PD, Weider LJ. Paleogenetic records of Daphnia pulicaria in two North American lakes reveal the impact of cultural eutrophication. GLOBAL CHANGE BIOLOGY 2017; 23:708-718. [PMID: 27474788 DOI: 10.1111/gcb.13445] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Understanding the evolutionary consequences of the green revolution, particularly in wild populations, is an important frontier in contemporary biology. Because human impacts have occurred at varying magnitudes or time periods depending on the study ecosystem, evolutionary histories may vary considerably among populations. Paleogenetics in conjunction with paleolimnology enable us to associate microevolutionary dynamics with detailed information on environmental change. We used this approach to reconstruct changes in the temporal population genetic structure of the keystone zooplankton grazer, Daphnia pulicaria, using dormant eggs extracted from sediments in two Minnesota lakes (South Center, Hill). The extent of agriculture and human population density in the catchment of these lakes has differed markedly since European settlement in the late 19th century and is reflected in their environmental histories reconstructed here. The reconstructed environments of these two lakes differed strongly in terms of environmental stability and their associated patterns of Daphnia population structure. We detected long periods of stability in population structure and environmental conditions in South Center Lake that were followed by a dramatic temporal shift in population genetic structure after the onset of European settlement and industrialized agriculture in its watershed. In particular, we noted a 24.3-fold increase in phosphorus (P) flux between pre-European and modern sediment P accumulation rates (AR) in this lake. In contrast, no such shifts were detected in Hill Lake, where the watershed was not as impacted by European settlement and rates of change were less directional with a much smaller increase in sediment P AR (2.3-fold). We identify direct and indirect effects of eutrophication proxies on genetic structure in these lake populations and demonstrate the power of using this approach in understanding the consequences of anthropogenic environmental change on natural populations throughout historic time periods.
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Affiliation(s)
- Dagmar Frisch
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Philip K Morton
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
- Division of Science, Murray State College, Tishomingo, OK, 73460, USA
| | - Billy W Culver
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
| | - Mark B Edlund
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, MN, 55047, USA
| | - Punidan D Jeyasingh
- Oklahoma State University, Department of Integrative Biology, Stillwater, OK, 74078, USA
| | - Lawrence J Weider
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73071, USA
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25
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Abstract
The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, 1205 avenue docteur Penfield, Montreal, Quebec, Canada H3A 1B1
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26
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Muñoz J, Chaturvedi A, De Meester L, Weider LJ. Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS). Sci Rep 2016; 6:28569. [PMID: 27346179 PMCID: PMC4921830 DOI: 10.1038/srep28569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/01/2016] [Indexed: 12/01/2022] Open
Abstract
The keystone aquatic herbivore Daphnia has been studied for more than 150 years in the context of evolution, ecology and ecotoxicology. Although it is rapidly becoming an emergent model for environmental and population genomics, there have been limited genome-wide level studies in natural populations. We report a unique resource of novel Single Nucleotide Polymorphic (SNP) markers for Daphnia pulicaria using the reduction in genomic complexity with the restriction enzymes approach, genotyping-by-sequencing. Using the genome of D. pulex as a reference, SNPs were scored for 53 clones from five natural populations that varied in lake trophic status. Our analyses resulted in 32,313 highly confident and bi-allelic SNP markers. 1,364 outlier SNPs were mapped on the annotated D. pulex genome, which identified 2,335 genes, including 565 within functional genes. Out of 885 EuKaryotic Orthologous Groups that we found from outlier SNPs, 294 were involved in three metabolic and four regulatory pathways. Bayesian-clustering analyses showed two distinct population clusters representing the possible combined effects of geography and lake trophic status. Our results provide an invaluable tool for future population genomics surveys in Daphnia targeting informative regions related to physiological processes that can be linked to the ecology of this emerging eco-responsive taxon.
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Affiliation(s)
- Joaquín Muñoz
- Doñana Biological Station (CSIC), Isla de La Cartuja, Av. Américo Vespucio S/N, 41092-Seville, Spain.,Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Anurag Chaturvedi
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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27
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Asselman J, De Coninck DIM, Pfrender ME, De Schamphelaere KAC. Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size. Genome Biol Evol 2016; 8:1185-96. [PMID: 27017526 PMCID: PMC4860698 DOI: 10.1093/gbe/evw069] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The relation between gene body methylation and gene function remains elusive. Yet, our understanding of this relationship can contribute significant knowledge on how and why organisms target specific gene bodies for methylation. Here, we studied gene body methylation patterns in two Daphnia species. We observed both highly methylated genes and genes devoid of methylation in a background of low global methylation levels. A small but highly significant number of genes was highly methylated in both species. Remarkably, functional analyses indicate that variation in methylation within and between Daphnia species is primarily targeted to small gene families whereas large gene families tend to lack variation. The degree of sequence similarity could not explain the observed pattern. Furthermore, a significant negative correlation between gene family size and the degree of methylation suggests that gene body methylation may help regulate gene family expansion and functional diversification of gene families leading to phenotypic variation.
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Affiliation(s)
- Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium Department of Biological Sciences, University of Notre Dame
| | - Dieter I M De Coninck
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium Laboratory of Pharmaceutical Biotechnology (labFBT), Ghent University, Ghent, Belgium
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame Environmental Change Initiative, University of Notre Dame
| | - Karel A C De Schamphelaere
- Laboratory for Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit (GhEnToxLab), Ghent University, Ghent, Belgium
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28
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Snell-Rood E, Cothran R, Espeset A, Jeyasingh P, Hobbie S, Morehouse NI. Life-history evolution in the anthropocene: effects of increasing nutrients on traits and trade-offs. Evol Appl 2015; 8:635-49. [PMID: 26240602 PMCID: PMC4516417 DOI: 10.1111/eva.12272] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/22/2015] [Indexed: 01/15/2023] Open
Abstract
Variation in life-history traits can have major impacts on the ecological and evolutionary responses of populations to environmental change. Life-history variation often results from trade-offs that arise because individuals have a limited pool of resources to allocate among traits. However, human activities are increasing the availability of many once-limited resources, such as nitrogen and phosphorus, with potentially major implications for the expression and evolution of life-history trade-offs. In this review, we synthesize contemporary life history and sexual selection literature with current research on ecosystem nutrient cycling to highlight novel opportunities presented by anthropogenic environmental change for investigating life-history trait development and evolution. Specifically, we review four areas where nutrition plays a pivotal role in life-history evolution and explore possible implications in the face of rapid, human-induced change in nutrient availability. For example, increases in the availability of nutrients may relax historical life-history trade-offs and reduce the honesty of signaling systems. We argue that ecosystems experiencing anthropogenic nutrient inputs present a powerful yet underexplored arena for testing novel and longstanding questions in organismal life-history evolution.
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Affiliation(s)
- Emilie Snell-Rood
- Department of Ecology, Evolution and Behavior, University of MinnesotaTwin Cities, MN, USA
| | - Rickey Cothran
- Department of Biological Sciences, University of PittsburghPittsburgh, PA, USA
- Department of Biological Sciences, Southwestern Oklahoma State UniversityWeatherford, OK, USA
| | - Anne Espeset
- Department of Ecology, Evolution and Behavior, University of MinnesotaTwin Cities, MN, USA
- Department of Biology, University of NevadaReno, NV, USA
| | | | - Sarah Hobbie
- Department of Ecology, Evolution and Behavior, University of MinnesotaTwin Cities, MN, USA
| | - Nathan I Morehouse
- Department of Biological Sciences, University of PittsburghPittsburgh, PA, USA
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Otte KA, Schrank I, Fröhlich T, Arnold GJ, Laforsch C. Interclonal proteomic responses to predator exposure inDaphnia magnamay depend on predator composition of habitats. Mol Ecol 2015; 24:3901-17. [DOI: 10.1111/mec.13287] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Kathrin A. Otte
- Laboratory for Functional Genome Analysis (LAFUGA); Gene Center; Ludwig-Maximilians-University Munich; Feodor-Lynen-Strasse 25 81377 Munich Germany
- Department Biology II; Ludwig Maximilians University Munich; Grosshaderner Street 2 82152 Planegg-Martinsried Germany
- Animal Ecology I and BayCEER; University of Bayreuth; Universitätsstrasse 30 95440 Bayreuth Germany
| | - Isabella Schrank
- Animal Ecology I and BayCEER; University of Bayreuth; Universitätsstrasse 30 95440 Bayreuth Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA); Gene Center; Ludwig-Maximilians-University Munich; Feodor-Lynen-Strasse 25 81377 Munich Germany
| | - Georg J. Arnold
- Laboratory for Functional Genome Analysis (LAFUGA); Gene Center; Ludwig-Maximilians-University Munich; Feodor-Lynen-Strasse 25 81377 Munich Germany
| | - Christian Laforsch
- Animal Ecology I and BayCEER; University of Bayreuth; Universitätsstrasse 30 95440 Bayreuth Germany
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Simpson AM, Jeyasingh PD, Belden JB. Variation in toxicity of a current-use insecticide among resurrected Daphnia pulicaria genotypes. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:488-496. [PMID: 25481822 DOI: 10.1007/s10646-014-1397-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
This study examined how genotypes of Daphnia pulicaria from a single population, separated by thousands of generations of evolution in the wild, differ in their sensitivity to a novel anthropogenic stressor. These genotypes were resurrected from preserved resting eggs isolated from sediments belonging to three time periods: 2002-2008, 1967-1977, and 1301-1646 A.D. Toxicity of the organophosphate insecticide chlorpyrifos was determined through a series of acute toxicity tests. There was a significant dose-response effect in all genotypes studied. Moreover, significant variation in toxicity among genotypes within each time period was detected. Importantly, a significant effect of time period on sensitivity to chlorpyrifos was found. Analysis of the median effect concentrations (EC50s) for genotypes within each time period indicated that the 1301-1646 genotypes were 2.7 times more sensitive than the 1967-1977 genotypes. This trend may be partially explained by microevolutionary shifts in response to cultural eutrophication.
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Affiliation(s)
- Adam M Simpson
- Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK, 74078, USA,
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