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Beam TC, Bright M, Pearson AC, Dua I, Smith M, Dutta AK, Bhadra SC, Salman S, Strickler CN, Anderson CE, Peshkin L, Yampolsky LY. Short lifespan is one's fate, long lifespan is one's achievement: lessons from Daphnia. GeroScience 2024:10.1007/s11357-024-01244-7. [PMID: 38900345 DOI: 10.1007/s11357-024-01244-7] [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: 04/30/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Studies of longevity rely on baseline life expectancy of reference genotypes measured in standardized conditions. Variation among labs, protocols, and genotypes makes longevity intervention studies difficult to compare. Furthermore, extending lifespan under suboptimal conditions or that of a short-lived genotype may be of a lesser theoretical and translational value than extending the maximal possible lifespan. Daphnia is becoming a model organism of choice for longevity research complementing data obtained on traditional models. In this study, we report longevity of several genotypes of a long-lived species D. magna under a variety of protocols, aiming to document the highest lifespan, factors reducing it, and parameters that change with age and correlate with longevity. Combining longevity data from 25 experiments across two labs, we report a strong intraspecific variation, moderate effects of group size and medium composition, and strong genotype-by-environment interactions with respect to food level. Specifically, short-lived genotypes show no caloric restriction (CR) effect, while long-lived ones expand their lifespan even further under CR. We find that the CR non-responsive clones show little correlation between longevity and two measures of lipid peroxidation. In contrast, the long-lived, CR-responsive clones show a positive correlation between longevity and lipid hydroperoxide abundance, and a negative correlation with MDA concentration. This indicates differences among genotypes in age-related accumulation and detoxification of LPO products and their effects on longevity. Our observations support the hypothesis that a long lifespan can be affected by CR and levels of oxidative damage, while genetically determined short lifespan remains short regardless.
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Affiliation(s)
- Thomas C Beam
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Mchale Bright
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Amelia C Pearson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ishaan Dua
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Meridith Smith
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Ashit K Dutta
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Shymal C Bhadra
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN, 46805, USA
| | - Saad Salman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Caleb N Strickler
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
| | - Cora E Anderson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37601, USA.
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2
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Lack of age-related respiratory changes in Daphnia. Biogerontology 2022; 23:85-97. [PMID: 34989913 DOI: 10.1007/s10522-021-09947-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/23/2021] [Indexed: 12/29/2022]
Abstract
Aging is a multifaceted process of accumulation of damage and waste in cells and tissues; age-related changes in mitochondria and in respiratory metabolism have the focus of aging research for decades. Studies of aging in nematodes, flies and mammals all revealed age-related decline in respiratory functions, with somewhat controversial causative role. Here we investigated age-related changes in respiration rates, lactate/pyruvate ratio, a commonly used proxy for NADH/NAD+ balance, and mitochondrial membrane potential in 4 genotypes of an emerging model organism for aging research, a cyclic parthenogen Daphnia magna. We show that total body weight-adjusted respiration rate decreased with age, although this decrease was small in magnitude and could be fully accounted for by the decrease in locomotion and feeding activity. Neither total respiration normalized by protein content, nor basal respiration rate measured in anaesthetized animals decreased with age. Lactate/pyruvate ratio and mitochondrial membrane potential (∆Ψmt) showed no age-related changes, with possible exceptions of ∆Ψmt in epipodites (excretory and gas exchange organs) in which ∆Ψmt decreased with age and in the optical lobe of the brain, in which ∆Ψmt showed a maximum at middle age. We conclude that actuarial senescence in Daphnia is not caused by a decline in respiratory metabolism and discuss possible mechanisms of maintaining mitochondrial healthspan throughout the lifespan.
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3
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Schomaker RA, Dudycha JL. De novo transcriptome assembly of the green alga Ankistrodesmus falcatus. PLoS One 2021; 16:e0251668. [PMID: 33989339 PMCID: PMC8121315 DOI: 10.1371/journal.pone.0251668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.
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Affiliation(s)
- Rachel A Schomaker
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
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4
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Ellis LJA, Kissane S, Hoffman E, Valsami-Jones E, Brown JB, Colbourne JK, Lynch I. Multigenerational Exposure to Nano‐TiO
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Induces Ageing as a Stress Response Mitigated by Environmental Interactions. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202000083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Laura-Jayne A. Ellis
- School of Geography, Earth and Environmental Sciences University of Birmingham Birmingham B15 2TT UK
| | - Stephen Kissane
- Environmental Transcriptomics Facility School of Biosciences University of Birmingham Birmingham B15 2TT UK
| | - Elijah Hoffman
- Genome Dynamics Department Life Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences University of Birmingham Birmingham B15 2TT UK
| | - James B. Brown
- Environmental Transcriptomics Facility School of Biosciences University of Birmingham Birmingham B15 2TT UK
- Genome Dynamics Department Life Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - John K. Colbourne
- Environmental Transcriptomics Facility School of Biosciences University of Birmingham Birmingham B15 2TT UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences University of Birmingham Birmingham B15 2TT UK
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5
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Davenport ES, Agrelius TC, Harmon KB, Dudycha JL. Fitness effects of spontaneous mutations in a warming world. Evolution 2021; 75:1513-1524. [PMID: 33751559 PMCID: PMC8252619 DOI: 10.1111/evo.14208] [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] [Received: 10/16/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Spontaneous mutations fuel evolutionary processes and differ in consequence, but the consequences depend on the environment. Biophysical considerations of protein thermostability predict that warm temperatures may systematically increase the deleteriousness of mutation. We sought to test whether mutation reduced fitness more when measured in an environment that reflected climate change projections for temperature. We investigated the effects of spontaneous mutations on life history, size, and fitness in 21 mutation accumulation lines and 12 control lines of Daphnia pulex at standard and elevated (+4℃) temperatures. Warmer temperature accelerated life history and reduced body length and clutch sizes. Mutation led to reduced mean clutch sizes and fitness estimates at both temperatures. We found no evidence of a systematic temperature–mutation interaction on trait means, although some lines showed evidence of beneficial mutation at one temperature and deleterious mutation at the other. However, trait variances are also influenced by mutation, and we observed increased variances due to mutation for most traits. For variance of the intrinsic rate of increase and some reproductive traits, we found significant temperature–mutation interactions, with a larger increase due to mutation in the warmer environment. This suggests that selection on new mutations will be more efficient at elevated temperatures.
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Affiliation(s)
- Elizabeth S Davenport
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208.,Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109
| | - Trenton C Agrelius
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208
| | - Krista B Harmon
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208
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6
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Miklós M, Laczkó L, Sramkó G, Sebestyén F, Barta Z, Tökölyi J. Phenotypic plasticity rather than genotype drives reproductive choices in Hydra populations. Mol Ecol 2021; 30:1206-1222. [PMID: 33465828 DOI: 10.1111/mec.15810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 12/23/2020] [Accepted: 01/08/2021] [Indexed: 12/16/2022]
Abstract
Facultative clonality is associated with complex life cycles where sexual and asexual forms can be exposed to contrasting selection pressures. Facultatively clonal animals often have distinct developmental capabilities that depend on reproductive mode (e.g., negligible senescence and exceptional regeneration ability in asexual individuals, which are lacking in sexual individuals). Understanding how these differences in life history strategies evolved is hampered by limited knowledge of the population structure underlying sexual and asexual forms in nature. Here we studied genetic differentiation of coexisting sexual and asexual Hydra oligactis polyps, a freshwater cnidarian where reproductive mode-dependent life history patterns are observed. We collected asexual and sexual polyps from 13 Central European water bodies and used restriction-site associated DNA sequencing to infer population structure. We detected high relatedness among populations and signs that hydras might spread with resting eggs through zoochory. We found no genetic structure with respect to mode of reproduction (asexual vs. sexual). On the other hand, clear evidence was found for phenotypic plasticity in mode of reproduction, as polyps inferred to be clones differed in reproductive mode. Moreover, we detected two cases of apparent sex change (males and females found within the same clonal lineages) in this species with supposedly stable sexes. Our study describes population genetic structure in Hydra for the first time, highlights the role of phenotypic plasticity in generating patterns of life history variation, and contributes to understanding the evolution of reproductive mode-dependent life history variation in coexisting asexual and sexual forms.
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Affiliation(s)
- Máté Miklós
- MTA-DE Behavioral Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary.,Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary
| | - Levente Laczkó
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary.,MTA-DE "Lendület" Evolutionary Phylogenomics Research Group, Debrecen, Hungary.,Department of Botany, University of Debrecen, Debrecen, Hungary
| | - Gábor Sramkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group, Debrecen, Hungary.,Department of Botany, University of Debrecen, Debrecen, Hungary
| | - Flóra Sebestyén
- MTA-DE Behavioral Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary.,Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Barta
- MTA-DE Behavioral Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary
| | - Jácint Tökölyi
- MTA-DE Behavioral Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary
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7
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Maternal Responses and Adaptive Changes to Environmental Stress via Chronic Nanomaterial Exposure: Differences in Inter and Transgenerational Interclonal Broods of Daphnia magna. Int J Mol Sci 2020; 22:ijms22010015. [PMID: 33374973 PMCID: PMC7792578 DOI: 10.3390/ijms22010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
There is increasing recognition that environmental nano-biological interactions in model species, and the resulting effects on progeny, are of paramount importance for nanomaterial (NM) risk assessment. In this work, Daphnia magna F0 mothers were exposed to a range of silver and titanium dioxide NMs. The key biological life history traits (survival, growth and reproduction) of the F1 intergenerations, at the first (F1B1), third (F1B3) and fifth (F1B5) broods, were investigated. Furthermore, the F1 germlines of each of the three broods were investigated over 3 more generations (up to 25 days each) in continuous or removed-from NM exposure, to identify how the length of maternal exposure affects the resulting clonal broods. Our results show how daphnids respond to NM-induced stress, and how the maternal effects show trade-offs between growth, reproduction and survivorship. The F1B1 (and following germline) had the shortest F0 maternal exposure times to the NMs, and thus were the most sensitive showing reduced size and reproductive output. The F1B3 generation had a sub-chronic maternal exposure, whereas the F1B5 generation suffered chronic maternal exposure where (in most cases) the most compensatory adaptive effects were displayed in response to the prolonged NM exposure, including enhanced neonate output and reduced gene expression. Transgenerational responses of multiple germlines showed a direct link with maternal exposure time to 'sub-lethal' effect concentrations of NMs (identified from standard OECDs acute toxicity tests which chronically presented as lethal) including increased survival and production of males in the F1B3 and G1B5 germlines. This information may help to fine-tune environmental risk assessments of NMs and prediction of their impacts on environmental ecology.
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8
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Comparative proteomic analysis of senescence in the freshwater cladoceran Daphnia pulex. Comp Biochem Physiol B Biochem Mol Biol 2020; 239:110352. [DOI: 10.1016/j.cbpb.2019.110352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/16/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
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9
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Johnson AA, Shokhirev MN, Shoshitaishvili B. Revamping the evolutionary theories of aging. Ageing Res Rev 2019; 55:100947. [PMID: 31449890 DOI: 10.1016/j.arr.2019.100947] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/20/2019] [Accepted: 08/21/2019] [Indexed: 01/04/2023]
Abstract
Radical lifespan disparities exist in the animal kingdom. While the ocean quahog can survive for half a millennium, the mayfly survives for less than 48 h. The evolutionary theories of aging seek to explain why such stark longevity differences exist and why a deleterious process like aging evolved. The classical mutation accumulation, antagonistic pleiotropy, and disposable soma theories predict that increased extrinsic mortality should select for the evolution of shorter lifespans and vice versa. Most experimental and comparative field studies conform to this prediction. Indeed, animals with extreme longevity (e.g., Greenland shark, bowhead whale, giant tortoise, vestimentiferan tubeworms) typically experience minimal predation. However, data from guppies, nematodes, and computational models show that increased extrinsic mortality can sometimes lead to longer evolved lifespans. The existence of theoretically immortal animals that experience extrinsic mortality - like planarian flatworms, panther worms, and hydra - further challenges classical assumptions. Octopuses pose another puzzle by exhibiting short lifespans and an uncanny intelligence, the latter of which is often associated with longevity and reduced extrinsic mortality. The evolutionary response to extrinsic mortality is likely dependent on multiple interacting factors in the organism, population, and ecology, including food availability, population density, reproductive cost, age-mortality interactions, and the mortality source.
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Affiliation(s)
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Boris Shoshitaishvili
- Division of Literatures, Cultures, and Languages, Stanford University, Stanford, CA, United States
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10
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Affiliation(s)
- Matthias Galipaud
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
| | - Hanna Kokko
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
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11
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Cai M, Liu Z, Chen M, Huang Y, Zhang M, Jiao Y, Zhao Y. Changes in ultrastructure of gonads and external morphology during aging in the parthenogenetic cladoceran Daphnia pulex. Micron 2019; 122:1-7. [DOI: 10.1016/j.micron.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 01/23/2023]
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12
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Constantinou J, Sullivan J, Mirbahai L. Ageing differently: Sex-dependent ageing rates in Daphnia magna. Exp Gerontol 2019; 121:33-45. [PMID: 30922945 DOI: 10.1016/j.exger.2019.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/08/2019] [Accepted: 03/23/2019] [Indexed: 01/08/2023]
Abstract
Ageing is defined as the gradual decline of normal physiological functions in a time-dependent manner. Significant progress has been made in characterising the regulatory processes involved in the mechanisms of ageing which would have been hindered without the use of model organisms. Use of alternative model organisms greatly diversifies our understanding of different factors underpinning the ageing process and the potential translation for human application. Unique characteristics make Daphnia an attractive model organism for research into mechanisms underlying ageing, such as transparent body, short generation time, well-characterised methylome, regenerative capabilities and available naturally occurring ecotypes. Most interestingly, genetically identical female and male Daphnia have evolved different average lifespans, providing a unique opportunity for understanding the underlying mechanisms of ageing and regulation of lifespan. Investigating sex differences in longevity could provide insight into principal mechanisms of ageing and lifespan regulation. In this study we provide evidence in support of establishing genetically identical female and male Daphnia as unique and valuable resources for research into mechanisms of ageing and begin to delineate the mechanisms involved in sex differences in lifespan. We identify significant differences between genders in physiological markers such as lifespan, growth rate, heart rate and swimming speed in addition to molecular markers such as lipid peroxidation product accumulation, thiol content decline and age-dependent decline in DNA damage repair efficiency. Overall, our data indicates that investigating sex differences in longevity in the clonal organism Daphnia under controlled laboratory conditions can provide insight into principal mechanisms of ageing and lifespan regulation.
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Affiliation(s)
- Julia Constantinou
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Jack Sullivan
- MRC-ARUK Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham B15 2WB, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
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13
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Pietrzak B, Grzesiuk M, Dorosz J, Mikulski A. When males outlive females: Sex-specific effects of temperature on lifespan in a cyclic parthenogen. Ecol Evol 2018; 8:9880-9888. [PMID: 30386583 PMCID: PMC6202703 DOI: 10.1002/ece3.4473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 03/26/2018] [Accepted: 06/27/2018] [Indexed: 12/16/2022] Open
Abstract
Lifespans of males and females frequently differ as a consequence of different life history strategies adopted to maximize fitness. It is well visible in cyclic parthenogens, such as water fleas of the genus Daphnia, where males appear in the population usually only for periods when receptive females are available. Moreover, even within one sex, different life history strategies and mechanisms regulating lifespan may exist. Previous studies suggested that Daphnia males may regulate their lifespan by staying in colder waters than females. We hypothesize that such behavioral mechanism should be associated with stronger reaction to low temperature-that is greater lifespan extension in males than in females. In this study, we monitored survivorship of Daphnia magna females and males of three clonal lines cultured at 16 or 20°C. The results did not provide a species-level corroboration of our hypothesis; instead, they revealed very strong intraspecific differences in the responses of male and female lifespan to temperature change. They further suggest the existence of parallel life history strategies, hypothesis whose tests would bring new insights into the ecology of males in cyclic parthenogens.
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Affiliation(s)
- Barbara Pietrzak
- Department of HydrobiologyFaculty of BiologyUniversity of Warsaw at Biological and Chemical Research CentreWarsawPoland
| | - Małgorzata Grzesiuk
- Department of HydrobiologyFaculty of BiologyUniversity of Warsaw at Biological and Chemical Research CentreWarsawPoland
| | - Julia Dorosz
- Department of HydrobiologyFaculty of BiologyUniversity of Warsaw at Biological and Chemical Research CentreWarsawPoland
| | - Andrzej Mikulski
- Department of HydrobiologyFaculty of BiologyUniversity of Warsaw at Biological and Chemical Research CentreWarsawPoland
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14
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Kvist J, Gonçalves Athanàsio C, Shams Solari O, Brown JB, Colbourne JK, Pfrender ME, Mirbahai L. Pattern of DNA Methylation in Daphnia: Evolutionary Perspective. Genome Biol Evol 2018; 10:1988-2007. [PMID: 30060190 PMCID: PMC6097596 DOI: 10.1093/gbe/evy155] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, we explore the DNA methylation profile of two species of the crustacean Daphnia using whole genome bisulfite sequencing. We then compare our data with the methylomes of two insects and two mammals to achieve a better understanding of the function of DNA methylation in Daphnia. Using RNA-sequencing data for all six species, we investigate the correlation between DNA methylation and gene expression. DNA methylation in Daphnia is mainly enriched within the coding regions of genes, with the highest methylation levels observed at exons 2–4. In contrast, vertebrate genomes are globally methylated, and increase towards the highest methylation levels observed at exon 2, and maintained across the rest of the gene body. Although DNA methylation patterns differ among all species, their methylation profiles share a bimodal distribution across the genomes. Genes with low levels of CpG methylation and gene expression are mainly enriched for species specific genes. In contrast, genes associated with high methylated CpG sites are highly transcribed and evolutionary conserved across all species. Finally, the positive correlation between internal exons and gene expression potentially points to an evolutionary conserved mechanism, whereas the negative regulation of gene expression via methylation of promoters and exon 1 is potentially a secondary mechanism that has been evolved in vertebrates.
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Affiliation(s)
- Jouni Kvist
- School of Biosciences, University of Birmingham, United Kingdom
| | | | | | - James B Brown
- Department of Statistics, University of California, Berkeley.,Centre for Computational Biology (CCB), University of Birmingham, United Kingdom
| | | | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
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15
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Dańko MJ, Burger O, Kozłowski J. Density-dependence interacts with extrinsic mortality in shaping life histories. PLoS One 2017; 12:e0186661. [PMID: 29049399 PMCID: PMC5648222 DOI: 10.1371/journal.pone.0186661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/05/2017] [Indexed: 12/02/2022] Open
Abstract
The role of extrinsic mortality in shaping life histories is poorly understood. However, substantial evidence suggests that extrinsic mortality interacts with density-dependence in crucial ways. We develop a model combining Evolutionarily Stable Strategies with a projection matrix that allows resource allocation to growth, tissue repairs, and reproduction. Our model examines three cases, with density-dependence acting on: (i) mortality, (ii) fecundity, and (iii) production rate. We demonstrate that density-independent extrinsic mortality influences the rate of aging, age at maturity, growth rate, and adult size provided that density-dependence acts on fertility or juvenile mortality. However, density-independent extrinsic mortality has no effect on these life history traits when density-dependence acts on survival. We show that extrinsic mortality interacts with density-dependence via a compensation mechanism: the higher the extrinsic mortality the lower the strength of density-dependence. However, this compensation fully offsets the effect of extrinsic mortality only if density-dependence acts on survival independently of age. Both the age-pattern and the type of density-dependence are crucial for shaping life history traits.
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Affiliation(s)
- Maciej Jan Dańko
- Max Planck Institute for Demographic Research, Rostock, Germany
- * E-mail:
| | - Oskar Burger
- Max Planck Institute for Demographic Research, Rostock, Germany
| | - Jan Kozłowski
- Jagiellonian University, Institute of Environmental Sciences, Kraków, Poland
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16
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Kiørboe T, Ceballos S, Thygesen UH. Interrelations between senescence, life-history traits, and behavior in planktonic copepods. Ecology 2015; 96:2225-35. [PMID: 26405747 DOI: 10.1890/14-2205.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The optimal allocation of resources to repair vs. reproduction in an organism may depend on the magnitude and pattern of the external mortality it is experiencing, which, in turn, may depend on its feeding and mate-finding behavior. Thus, the fundamental activities of an organism, i.e., to feed, to survive, and to reproduce, are interrelated through trade-offs. Here, we use small planktonic copepods to examine how adult longevity and ageing patterns in a protected laboratory environment relate to the feeding mode (active searching vs. passive ambush feeding), mate-finding behavior, and spawning mode of the species. We show that average adult longevity varies between species by an order of magnitude and is independent of body size. Ambush feeders that carry their eggs have longer average life spans and experience higher mortality later in life relative to active feeders that broadcast their eggs. Males generally have shorter life spans and experience higher mortality earlier in life than females, and this difference may be accentuated in species where dangerous mate-finding is male biased. We finally show a trade-off between longevity and fecundity, with ambush feeders producing eggs at a rate five to 10 times lower than the active feeders, consistent with predictions from optimal resource allocation theory.
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Schumpert CA, Dudycha JL, Patel RC. Development of an efficient RNA interference method by feeding for the microcrustacean Daphnia. BMC Biotechnol 2015; 15:91. [PMID: 26446824 PMCID: PMC4597761 DOI: 10.1186/s12896-015-0209-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/01/2015] [Indexed: 12/18/2022] Open
Abstract
Background RNA interference (RNAi) is an important molecular tool for analysis of gene function in vivo. Daphnia, a freshwater microcrustacean, is an emerging model organism for studying cellular and molecular processes involved in aging, development, and ecotoxicology especially in the context of environmental variation. However, in spite of the availability of a fully sequenced genome of Daphnia pulex, meaningful mechanistic studies have been hampered by a lack of molecular techniques to alter gene expression. A microinjection method for gene knockdown by RNAi has been described but the need for highly specialized equipment as well as technical expertise limits the wider application of this technique. In addition to being expensive and technically challenging, microinjections can only target genes expressed during embryonic stages, thus making it difficult to achieve effective RNAi in adult organisms. Results In our present study we present a bacterial feeding method for RNAi in Daphnia. We used a melanic Daphnia species (Daphnia melanica) that exhibits dark pigmentation to target phenoloxidase, a key enzyme in the biosynthesis of melanin. We demonstrate that our RNAi method results in a striking phenotype and that the phenoloxidase mRNA expression and melanin content, as well as survival following UV insults, are diminished as a result of RNAi. Conclusions Overall, our results establish a new method for RNAi in Daphnia that significantly advances further use of Daphnia as a model organism for functional genomics studies. The method we describe is relatively simple and widely applicable for knockdown of a variety of genes in adult organisms.
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Affiliation(s)
- Charles A Schumpert
- Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC, 29208, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC, 29208, USA
| | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC, 29208, USA.
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Abstract
Telomeres, comprised of short repetitive sequences, are essential for genome stability and have been studied in relation to cellular senescence and aging. Telomerase, the enzyme that adds telomeric repeats to chromosome ends, is essential for maintaining the overall telomere length. A lack of telomerase activity in mammalian somatic cells results in progressive shortening of telomeres with each cellular replication event. Mammals exhibit high rates of cell proliferation during embryonic and juvenile stages but very little somatic cell proliferation occurs during adult and senescent stages. The telomere hypothesis of cellular aging states that telomeres serve as an internal mitotic clock and telomere length erosion leads to cellular senescence and eventual cell death. In this report, we have examined telomerase activity, processivity, and telomere length in Daphnia, an organism that grows continuously throughout its life. Similar to insects, Daphnia telomeric repeat sequence was determined to be TTAGG and telomerase products with five-nucleotide periodicity were generated in the telomerase activity assay. We investigated telomerase function and telomere lengths in two closely related ecotypes of Daphnia with divergent lifespans, short-lived D. pulex and long-lived D. pulicaria. Our results indicate that there is no age-dependent decline in telomere length, telomerase activity, or processivity in short-lived D. pulex. On the contrary, a significant age dependent decline in telomere length, telomerase activity and processivity is observed during life span in long-lived D. pulicaria. While providing the first report on characterization of Daphnia telomeres and telomerase activity, our results also indicate that mechanisms other than telomere shortening may be responsible for the strikingly short life span of D. pulex.
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Lohr JN, David P, Haag CR. Reduced lifespan and increased ageing driven by genetic drift in small populations. Evolution 2014; 68:2494-508. [PMID: 24897994 DOI: 10.1111/evo.12464] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 05/15/2014] [Indexed: 11/28/2022]
Abstract
Explaining the strong variation in lifespan among organisms remains a major challenge in evolutionary biology. Whereas previous work has concentrated mainly on differences in selection regimes and selection pressures, we hypothesize that differences in genetic drift may explain some of this variation. We develop a model to formalize this idea and show that the strong positive relationship between lifespan and genetic diversity predicted by this model indeed exists among populations of Daphnia magna, and that ageing is accelerated in small populations. Additional results suggest that this is due to increased drift in small populations rather than adaptation to environments favoring faster life histories. First, the correlation between genetic diversity and lifespan remains significant after statistical correction for potential environmental covariates. Second, no trade-offs are observed; rather, all investigated traits show clear signs of increased genetic load in the small populations. Third, hybrid vigor with respect to lifespan is observed in crosses between small but not between large populations. Together, these results suggest that the evolution of lifespan and ageing can be strongly affected by genetic drift, especially in small populations, and that variation in lifespan and ageing may often be nonadaptive, due to a strong contribution from mutation accumulation.
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Affiliation(s)
- Jennifer N Lohr
- Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland; Tvärminne Zoological Station, FIN-10900, Hanko, Finland.
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Schumpert C, Handy I, Dudycha JL, Patel RC. Relationship between heat shock protein 70 expression and life span in Daphnia. Mech Ageing Dev 2014; 139:1-10. [PMID: 24814302 DOI: 10.1016/j.mad.2014.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 04/23/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
The longevity of an organism is directly related to its ability to effectively cope with cellular stress. Heat shock response (HSR) protects the cells against accumulation of damaged proteins after exposure to elevated temperatures and also in aging cells. To understand the role of Hsp70 in regulating life span of Daphnia, we examined the expression of Hsp70 in two ecotypes that exhibit strikingly different life spans. Daphnia pulicaria, the long lived ecotype, showed a robust Hsp70 induction as compared to the shorter lived Daphnia pulex. Interestingly, the short-lived D. pulex isolates showed no induction of Hsp70 at the mid point in their life span. In contrast to this, the long-lived D. pulicaria continued to induce Hsp70 expression at an equivalent age. We further show that the Hsp70 expression was induced at transcriptional level in response to heat shock. The transcription factor responsible for Hsp70 induction, heat shock factor-1 (HSF-1), although present in aged organisms did not exhibit DNA-binding capability. Thus, the decline of Hsp70 induction in old organisms could be attributed to a decline in HSF-1's DNA-binding activity. These results for the first time, present a molecular analysis of the relationship between HSR and life span in Daphnia.
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Affiliation(s)
- Charles Schumpert
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Indhira Handy
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States
| | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States.
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Smith HA, Snell TW. Differential evolution of asexual and sexual females in a benign culture environment. INTERNATIONAL REVIEW OF HYDROBIOLOGY 2014; 99:117-124. [PMID: 24795527 PMCID: PMC4004349 DOI: 10.1002/iroh.201301711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here we report one of the first investigations of evolvability of lifespan and reproduction in metazoans, examining both extrinsic and intrinsic factors. We tested effects on senescence of an environmental variable (simulated lake hydroperiod, the length of time an aquatic habitat is inundated), female reproductive physiology (asexual females that reproduce by ameiosis, versus sexual females reproducing by meiosis), and time in a benign culture environment (minimal, if any, external mortality factors). To do this we established chemostat cultures of the rotifer Brachionus plicatilis s.s., and maintained the cultures for 385 d. Hydroperiod alone or in interaction with the effects of time in the benign environment (season) or reproductive physiology had no significant effect on the net reproductive rate, generation time, or rate of aging. Yet combining animals from both ephemeral and permanent hydroperiods revealed a 26% increase in asexual female lifespan across seasons (23% decrease in the rate of aging) and a 56% increase in asexual fecundity, suggesting that maintenance in benign laboratory conditions leads to slower aging. The relative stasis of traits for sexual females implies an impact of reproductive physiology on evolvability. In addition we found a positive correlation between fecundity and lifespan, suggesting an absence of trade-offs in life history traits in the benign laboratory environment.
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Affiliation(s)
- Hilary A. Smith
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556-0369, USA
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Terry W. Snell
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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Effects of extrinsic mortality on the evolution of aging: a stochastic modeling approach. PLoS One 2014; 9:e86602. [PMID: 24466165 PMCID: PMC3897743 DOI: 10.1371/journal.pone.0086602] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/13/2013] [Indexed: 11/19/2022] Open
Abstract
The evolutionary theories of aging are useful for gaining insights into the complex mechanisms underlying senescence. Classical theories argue that high levels of extrinsic mortality should select for the evolution of shorter lifespans and earlier peak fertility. Non-classical theories, in contrast, posit that an increase in extrinsic mortality could select for the evolution of longer lifespans. Although numerous studies support the classical paradigm, recent data challenge classical predictions, finding that high extrinsic mortality can select for the evolution of longer lifespans. To further elucidate the role of extrinsic mortality in the evolution of aging, we implemented a stochastic, agent-based, computational model. We used a simulated annealing optimization approach to predict which model parameters predispose populations to evolve longer or shorter lifespans in response to increased levels of predation. We report that longer lifespans evolved in the presence of rising predation if the cost of mating is relatively high and if energy is available in excess. Conversely, we found that dramatically shorter lifespans evolved when mating costs were relatively low and food was relatively scarce. We also analyzed the effects of increased predation on various parameters related to density dependence and energy allocation. Longer and shorter lifespans were accompanied by increased and decreased investments of energy into somatic maintenance, respectively. Similarly, earlier and later maturation ages were accompanied by increased and decreased energetic investments into early fecundity, respectively. Higher predation significantly decreased the total population size, enlarged the shared resource pool, and redistributed energy reserves for mature individuals. These results both corroborate and refine classical predictions, demonstrating a population-level trade-off between longevity and fecundity and identifying conditions that produce both classical and non-classical lifespan effects.
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