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Scheffer H, Coate JE, Ho EKH, Schaack S. Thermal stress and mutation accumulation increase heat shock protein expression in Daphnia. Evol Ecol 2022; 36:829-844. [PMID: 36193163 PMCID: PMC9522699 DOI: 10.1007/s10682-022-10209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/25/2022] [Indexed: 11/28/2022]
Abstract
Understanding the short- and long-term consequences of climate change is a major challenge in biology. For aquatic organisms, temperature changes and drought can lead to thermal stress and habitat loss, both of which can ultimately lead to higher mutation rates. Here, we examine the effect of high temperature and mutation accumulation on gene expression at two loci from the heat shock protein (HSP) gene family, HSP60 and HSP90. HSPs have been posited to serve as 'mutational capacitors' given their role as molecular chaperones involved in protein folding and degradation, thus buffering against a wide range of cellular stress and destabilization. We assayed changes in HSP expression across 5 genotypes of Daphnia magna, a sentinel species in ecology and environmental biology, with and without acute exposure to thermal stress and accumulated mutations. Across genotypes, HSP expression increased ~ 6× in response to heat and ~ 4× with mutation accumulation, individually. Both factors simultaneously (lineages with high mutation loads exposed to high heat) increased gene expression ~ 23×-much more than that predicted by an additive model. Our results corroborate suggestions that HSPs can buffer against not only the effects of heat, but also mutations-a combination of factors both likely to increase in a warming world. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10209-1.
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Affiliation(s)
- Henry Scheffer
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Jeremy E. Coate
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Eddie K. H. Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
| | - Sarah Schaack
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202 USA
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2
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Ho EKH, Schaack S. Intraspecific Variation in the Rates of Mutations Causing Structural Variation in Daphnia magna. Genome Biol Evol 2021; 13:6444992. [PMID: 34849778 PMCID: PMC8691059 DOI: 10.1093/gbe/evab241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations that cause structural variation are important sources of genetic variation upon which other evolutionary forces can act, however, they are difficult to observe and therefore few direct estimates of their rate and spectrum are available. Understanding mutation rate evolution, however, requires adding to the limited number of species for which direct estimates are available, quantifying levels of intraspecific variation in mutation rates, and assessing whether rate estimates co-vary across types of mutation. Here, we report structural variation-causing mutation rates (svcMRs) for six categories of mutations (short insertions and deletions, long deletions and duplications, and deletions and duplications at copy number variable sites) from nine genotypes of Daphnia magna collected from three populations in Finland, Germany, and Israel using a mutation accumulation approach. Based on whole-genome sequence data and validated using simulations, we find svcMRs are high (two orders of magnitude higher than base substitution mutation rates measured in the same lineages), highly variable among populations, and uncorrelated across categories of mutation. Furthermore, to assess the impact of scvMRs on the genome, we calculated rates while adjusting for the lengths of events and ran simulations to determine if the mutations occur in genic regions more or less frequently than expected by chance. Our results pose a challenge to most prevailing theories aimed at explaining the evolution of the mutation rate, underscoring the importance of obtaining additional mutation rate estimates in more genotypes, for more types of mutation, in more species, in order to improve our future understanding of mutation rates, their variation, and their evolution.
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Affiliation(s)
- Eddie K H Ho
- Department of Biology, Reed College, Portland, Oregon, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, Oregon, USA
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3
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Ho EKH, Bellis ES, Calkins J, Adrion JR, Latta IV LC, Schaack S. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna. PLoS Genet 2021; 17:e1009827. [PMID: 34723969 PMCID: PMC8594854 DOI: 10.1371/journal.pgen.1009827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10-5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.
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Affiliation(s)
- Eddie K. H. Ho
- Department of Biology, Reed College, Portland, Oregon, United States of America
| | - Emily S. Bellis
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Jaclyn Calkins
- Department of Biology, Reed College, Portland, Oregon, United States of America
- College of Human Medicine, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey R. Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Leigh C. Latta IV
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Lewis-Clark State College, Lewiston, Idaho, United States of America
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, Oregon, United States of America
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4
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Breitholtz M, Ivanov P, Ek K, Gorokhova E. Calmodulin inhibition as a mode of action of antifungal imidazole pharmaceuticals in non-target organisms. Toxicol Res (Camb) 2020; 9:425-430. [PMID: 32905197 PMCID: PMC7467228 DOI: 10.1093/toxres/tfaa039] [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: 12/19/2019] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 01/08/2023] Open
Abstract
To improve assessment of risks associated with pharmaceutical contamination of the environment, it is crucial to understand effects and mode of action of drugs in non-target species. The evidence is accumulating that species with well-conserved drug targets are prone to be at risk when exposed to pharmaceuticals. An interesting group of pharmaceuticals released into the environment is imidazoles, antifungal agents with inhibition of ergosterol synthesis as a primary mode of action in fungi. However, imidazoles have also been identified as competitive antagonists of calmodulin (CaM), a calcium-binding protein with phylogenetically conserved structure and function. Therefore, imidazoles would act as CaM inhibitors in various organisms, including those with limited capacity to synthesize sterols, such as arthropods. We hypothesized that effects observed in crustaceans exposed to imidazoles are related to the CaM inhibition and CaM-dependent nitric oxide (NO) synthesis. To test this hypothesis, we measured (i) CaM levels and its gene expression, (ii) NO accumulation and (iii) gene expression of NO synthase (NOS1 and NOS2), in the cladoceran Daphnia magna exposed to miconazole, a model imidazole drug. Whereas significantly increased CaM gene expression and its cellular allocation were observed, supporting the hypothesized mode of action, no changes occurred in either NO synthase expression or NO levels in the exposed animals. These findings suggest that CaM inhibition by miconazole leads to protein overexpression that compensates for the loss in the protein activity, with no measurable downstream effects on NO pathways. The inhibition of CaM in D. magna may have implications for effect assessment of exposure to mixtures of imidazoles in aquatic non-target species.
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Affiliation(s)
- Magnus Breitholtz
- Department of Environmental Science and Analytical Chemistry , Stockholm University, SE-106 91, Sweden
| | - Pavel Ivanov
- Department of Environmental Science and Analytical Chemistry , Stockholm University, SE-106 91, Sweden
| | - Karin Ek
- Department of Environmental Science and Analytical Chemistry , Stockholm University, SE-106 91, Sweden
| | - Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry , Stockholm University, SE-106 91, Sweden
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5
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Frankel-Bricker J, Song MJ, Benner MJ, Schaack S. Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature. MICROBIAL ECOLOGY 2020; 79:731-742. [PMID: 31377832 PMCID: PMC7176607 DOI: 10.1007/s00248-019-01412-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/04/2019] [Indexed: 05/09/2023]
Abstract
Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.
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Affiliation(s)
- Jonas Frankel-Bricker
- Department of Biology, Reed College, Portland, OR, 97202, USA
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Michael J Song
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Maia J Benner
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, 97202, USA.
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6
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Ho EKH, Macrae F, Latta LC, Benner MJ, Sun C, Ebert D, Schaack S. Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna. Mol Biol Evol 2020; 36:1942-1954. [PMID: 31077327 PMCID: PMC6934441 DOI: 10.1093/molbev/msz118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.
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Affiliation(s)
- Eddie K H Ho
- Department of Biology, Reed College, Portland, OR
| | | | - Leigh C Latta
- Department of Biology, Reed College, Portland, OR
- Division of Natural Sciences and Mathematics, Lewis-Clark State College, Lewiston, ID
| | | | - Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR
- Corresponding author: E-mail:
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7
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Qin G, Xiong Y, Tang S, Zhao P, Doering JA, Beitel SC, Hecker M, Wang M, Liu H, Lu H, Du H. Impact of Predator Cues on Responses to Silver Nanoparticles in Daphnia carinata. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 69:494-505. [PMID: 26044927 DOI: 10.1007/s00244-015-0165-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
The past decades have witnessed a boom in nanotechnology that has led to increasing production and application of silver nanoparticles (AgNPs) in the textile industry due to their antimicrobial properties. Increase in the manufacture and use of NPs inevitably has resulted in their increased release into aquatic environments resulting in the exposure of organisms living in these environments. Recently, the risk of exposure to NPs and the potential interaction with biological systems has received increasing attention. The present study investigated the potential effects of predator cues on the toxicity of environmentally relevant concentrations of AgNPs in Daphnia carinata at organismal and biochemical levels. The results of this study show that exposure to environmentally relevant concentrations of AgNPs can result in adverse effects on daphnids with 24- and 48-h LC50 values of 3.56 and 1.75 μg/L, respectively. Furthermore, significant inhibition of reproduction was observed at concentrations as low as 0.5 μg/L. Exposure to predator cues alone resulted in an increase in reproduction and inhibition of superoxide dismutase activity in daphnids. However, coexposure to predator cues interacted in an antagonistic manner with AgNPs with a 24-h LC50 value of 10.81 μg/L compared with 3.56 μg/L for AgNPs alone. In summary, AgNPs could pose risks to aquatic invertebrates at environmentally relevant concentrations. Interestingly, the presence of other factors, such as predator cues, moderated the effects of exposure to AgNPs. Therefore, there is a need to further investigate the potential interactions between NPs and biological factors that can modulate toxicity of NPs for application to the risk assessment of aquatic invertebrates.
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Affiliation(s)
- Guangqiu Qin
- Institute of Toxicology, Guangxi Center for Disease Prevention and Control, Nanning, 530028, China.
| | - Yunxia Xiong
- College of Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Peng Zhao
- Institute of Toxicology, Guangxi Center for Disease Prevention and Control, Nanning, 530028, China
| | - Jon A Doering
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Shawn C Beitel
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Markus Hecker
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Mao Wang
- Department of Preventive Medicine, School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Haoliang Lu
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Huamao Du
- College of Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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8
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Rozenberg A, Parida M, Leese F, Weiss LC, Tollrian R, Manak JR. Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex. Front Zool 2015. [PMID: 26213557 PMCID: PMC4514973 DOI: 10.1186/s12983-015-0109-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Predator-induced defences are a prominent example of phenotypic plasticity found from single-celled organisms to vertebrates. The water flea Daphnia pulex is a very convenient ecological genomic model for studying predator-induced defences as it exhibits substantial morphological changes under predation risk. Most importantly, however, genetically identical clones can be transcriptionally profiled under both control and predation risk conditions and be compared due to the availability of the sequenced reference genome. Earlier gene expression analyses of candidate genes as well as a tiled genomic microarray expression experiment have provided insights into some genes involved in predator-induced phenotypic plasticity. Here we performed the first RNA-Seq analysis to identify genes that were differentially expressed in defended vs. undefended D. pulex specimens in order to explore the genetic mechanisms underlying predator-induced defences at a qualitatively novel level. Results We report 230 differentially expressed genes (158 up- and 72 down-regulated) identified in at least two of three different assembly approaches. Several of the differentially regulated genes belong to families of paralogous genes. The most prominent classes amongst the up-regulated genes include cuticle genes, zinc-metalloproteinases and vitellogenin genes. Furthermore, several genes from this group code for proteins recruited in chromatin-reorganization or regulation of the cell cycle (cyclins). Down-regulated gene classes include C-type lectins, proteins involved in lipogenesis, and other families, some of which encode proteins with no known molecular function. Conclusions The RNA-Seq transcriptome data presented in this study provide important insights into gene regulatory patterns underlying predator-induced defences. In particular, we characterized different effector genes and gene families found to be regulated in Daphnia in response to the presence of an invertebrate predator. These effector genes are mostly in agreement with expectations based on observed phenotypic changes including morphological alterations, i.e., expression of proteins involved in formation of protective structures and in cuticle strengthening, as well as proteins required for resource re-allocation. Our findings identify key genetic pathways associated with anti-predator defences. Electronic supplementary material The online version of this article (doi:10.1186/s12983-015-0109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey Rozenberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum, 44801 Germany
| | - Mrutyunjaya Parida
- Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USA
| | - Florian Leese
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum, 44801 Germany.,Present address: University of Duisburg-Essen, Aquatic Ecosystems Research, Universitaetsstrasse 5, Essen, 45141 Germany
| | - Linda C Weiss
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum, 44801 Germany.,Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, Bochum, 44801 Germany
| | - J Robert Manak
- Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USA
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Schaack S, Allen DE, Latta LC, Morgan KK, Lynch M. The effect of spontaneous mutations on competitive ability. J Evol Biol 2013; 26:451-6. [PMID: 23252614 PMCID: PMC3548015 DOI: 10.1111/jeb.12058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 12/11/2022]
Abstract
Understanding the impact of spontaneous mutations on fitness has many theoretical and practical applications in biology. Although mutational effects on individual morphological or life-history characters have been measured in several classic genetic model systems, there are few estimates of the rate of decline due to mutation for complex fitness traits. Here, we estimate the effects of mutation on competitive ability, an important complex fitness trait, in a model system for ecological and evolutionary genomics, Daphnia. Competition assays were performed to compare fitness between mutation-accumulation (MA) lines and control lines from eight different genotypes from two populations of Daphnia pulicaria after 30 and 65 generations of mutation accumulation. Our results show a fitness decline among MA lines relative to controls as expected, but highlight the influence of genomic background on this effect. In addition, in some assays, MA lines outperform controls providing insight into the frequency of beneficial mutations.
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Affiliation(s)
- S Schaack
- Department of Biology, Reed College, Portland, OR 97202, USA.
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10
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Beck JB, Allison JR, Pryer KM, Windham MD. Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1857-1865. [PMID: 23108464 DOI: 10.3732/ajb.1200199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Molecular studies have shown that multiple origins of polyploid taxa are the rule rather than the exception. To understand the distribution and ecology of polyploid species and the evolutionary significance of polyploidy in general, it is important to delineate these independently derived lineages as accurately as possible. Although gene flow among polyploid lineages and backcrossing to their diploid parents often confound this process, such post origin gene flow is very infrequent in asexual polyploids. In this study, we estimate the number of independent origins of the apomictic allopolyploid fern Astrolepis integerrima, a morphologically heterogeneous species most common in the southwestern United States and Mexico, with outlying populations in the southeastern United States and the Caribbean. METHODS Plastid DNA sequence and AFLP data were obtained from 33 A. integerrima individuals. Phylogenetic analysis of the sequence data and multidimensional clustering of the AFLP data were used to identify independently derived lineages. KEY RESULTS Analysis of the two datasets identified 10 genetic groups within the 33 analyzed samples. These groups suggest a minimum of 10 origins of A. integerrima in the northern portion of its range, with both putative parents functioning as maternal donors, both supplying unreduced gametes, and both contributing a significant portion of their genetic diversity to the hybrids. CONCLUSIONS Our results highlight the extreme cryptic genetic diversity and systematic complexity that can underlie a single polyploid taxon.
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MESH Headings
- Amplified Fragment Length Polymorphism Analysis
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Genes, Plant/genetics
- Geography
- Mexico
- Molecular Sequence Data
- Phylogeny
- Polyploidy
- Pteridaceae/classification
- Pteridaceae/genetics
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Gly/genetics
- Sequence Analysis, DNA
- United States
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Affiliation(s)
- James B Beck
- Department of Biological Sciences, Wichita State University, 537 Hubbard Hall, Wichita, Kansas 67260, USA.
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11
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Crease TJ, Omilian AR, Costanzo KS, Taylor DJ. Transcontinental phylogeography of the Daphnia pulex species complex. PLoS One 2012; 7:e46620. [PMID: 23056371 PMCID: PMC3463573 DOI: 10.1371/journal.pone.0046620] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022] Open
Abstract
Daphnia pulex is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the Daphnia pulex species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the D. pulex complex, and one lineage in particular, panarctic D. pulex, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the D. pulex complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the D. pulex complex. We found that the well-studied panarctic D. pulex is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic D. pulex--a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic D. pulex lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic D. pulex lineage warrants further study.
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Affiliation(s)
- Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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12
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McCoole MD, D'Andrea BT, Baer KN, Christie AE. Genomic analyses of gas (nitric oxide and carbon monoxide) and small molecule transmitter (acetylcholine, glutamate and GABA) signaling systems in Daphnia pulex. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:124-60. [DOI: 10.1016/j.cbd.2012.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/03/2012] [Accepted: 01/03/2012] [Indexed: 11/25/2022]
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13
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McCoole MD, Atkinson NJ, Graham DI, Grasser EB, Joselow AL, McCall NM, Welker AM, Wilsterman EJ, Baer KN, Tilden AR, Christie AE. Genomic analyses of aminergic signaling systems (dopamine, octopamine and serotonin) in Daphnia pulex. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:35-58. [DOI: 10.1016/j.cbd.2011.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/26/2011] [Accepted: 10/29/2011] [Indexed: 01/24/2023]
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McCoole MD, Baer KN, Christie AE. Histaminergic signaling in the central nervous system of Daphnia and a role for it in the control of phototactic behavior. ACTA ACUST UNITED AC 2011; 214:1773-82. [PMID: 21525325 DOI: 10.1242/jeb.054486] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Daphnia magna and Daphnia pulex are well-established model organisms in the fields of ecotoxicology and toxicogenomics. Among the many assays used for determining the effects of environmental and anthropogenic stressors on these animals is monitoring for changes in their phototactic behavior. In most arthropods, histamine has been shown to play a key role in the visual system. Currently, nothing is known about histaminergic signaling in either D. magna or D. pulex. Here, a combination of immunohistochemistry and genome mining was used to identify and characterize the histaminergic systems in these daphnids. In addition, a behavioral assay was used to assess the role of histamine in their phototactic response to ultraviolet (UV) light exposure. An extensive network of histaminergic somata, axons and neuropil was identified via immunohistochemistry within the central nervous system of both daphnids, including labeling of putative photoreceptors in the compound eye and projections from these cells to the brain. Mining of the D. pulex genome using known Drosophila melanogaster proteins identified a putative ortholog of histidine decarboxylase (the rate-limiting biosynthetic enzyme for histamine), as well as two putative histamine-gated chloride channels (hclA and hclB orthologs). Exposure of D. magna to cimetidine, an H2 receptor antagonist known to block both hclA and hclB in D. melanogaster, inhibited their negative phototactic response to UV exposure in a reversible, time-dependent manner. Taken collectively, our results show that an extensive histaminergic system is present in Daphnia species, including the visual system, and that this amine is involved in the control of phototaxis in these animals.
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Affiliation(s)
- Matthew D McCoole
- Department of Toxicology, College of Pharmacy, University of Louisiana at Monroe, 700 University Avenue, Monroe, LA 71209, USA
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Christie AE, McCoole MD, Harmon SM, Baer KN, Lenz PH. Genomic analyses of the Daphnia pulex peptidome. Gen Comp Endocrinol 2011; 171:131-50. [PMID: 21216245 DOI: 10.1016/j.ygcen.2011.01.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/23/2010] [Accepted: 01/01/2011] [Indexed: 11/22/2022]
Abstract
Genome mining has provided a valuable tool for peptide discovery in many species, yet no crustacean has undergone this analysis. Currently, the only crustacean with a sequenced genome is the cladoceran Daphnia pulex, a model organism in many fields of biology. Here, we have mined the D. pulex genome for peptide-encoding genes. For each gene identified, the encoded precursor protein was deduced, and its mature peptides predicted. Twenty-four peptide-encoding genes were identified, including ones predicted to produce members of the A-type allatostatin, B-type allatostatin, C-type allatostatin, allatotropin (ATR), bursicon α, bursicon β, calcitonin-like diuretic hormone, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone, ecdysis-triggering hormone, eclosion hormone (EH), insulin-like peptide (ILP), molt-inhibiting hormone, neuropeptide F, orcokinin (two genes), pigment-dispersing hormone, proctolin, red pigment concentrating hormone/adipokinetic hormone (RPCH/AKH), short neuropeptide F, SIFamide, sulfakinin, and tachykinin-related peptide (TRP) families/subfamilies. In total, 96 peptides were predicted from these genes. Our identification of isoforms of corazonin, EH, ILP, proctolin, RPCH/AKH, sulfakinin and TRP are the first for D. pulex, while our prediction of ATR from this species is the first from any crustacean. The number of peptides predicted in our study shows the power of genome mining for peptide discovery, and provides a model for future genomic analyses of the peptidomes of other crustaceans. In addition, the data presented in our study provide foundations for future molecular, biochemical, anatomical, and physiological investigation of peptidergic signaling in D. pulex and other cladoceran species.
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Affiliation(s)
- Andrew E Christie
- Neuroscience Program, John W. and Jean C. Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA.
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Christie AE, Durkin CS, Hartline N, Ohno P, Lenz PH. Bioinformatic analyses of the publicly accessible crustacean expressed sequence tags (ESTs) reveal numerous novel neuropeptide-encoding precursor proteins, including ones from members of several little studied taxa. Gen Comp Endocrinol 2010; 167:164-78. [PMID: 20064519 DOI: 10.1016/j.ygcen.2010.01.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/31/2009] [Accepted: 01/03/2010] [Indexed: 12/25/2022]
Abstract
ESTs have been generated for many crustacean species, providing an invaluable resource for peptide discovery in members of this arthropod subphylum. Here, these data were mined for novel peptide-encoding transcripts, with the mature peptides encoded by them predicted using a combination of online peptide prediction programs and homology to known arthropod sequences. In total, 70 mature full-length/partial peptides representing members of 16 families/subfamilies were predicted, the vast majority being novel; the species from which the peptides were identified included members of the Branchiopoda (Daphnia carinata and Triops cancriformis), Maxillopoda (Caligus clemensi, Caligus rogercresseyi, Lepeophtheirus salmonis and Lernaeocera branchialis) and Malacostraca (Euphausia superba, Marsupenaeus japonicus, Penaeus monodon, Homarus americanus, Petrolisthes cinctipes, Callinectes sapidus and Portunus trituberculatus). Of particular note were the identifications of an intermediate between the insect adipokinetic hormones and crustacean red pigment concentrating hormone and a modified crustacean cardioactive peptide from the daphnid D. carinata; Arg(7)-corazonin was also deduced from this species, the first identification of a corazonin from a non-decapod crustacean. Our data also include the first reports of members of the calcitonin-like diuretic hormone, FMRFamide-related peptide (neuropeptide F subfamily) and orcokinin families from members of the Copepoda. Moreover, the prediction of a bursicon alpha from the euphausid E. superba represents the first peptide identified from any member of the basal eucaridean order Euphausiacea. In addition, large collections of insect eclosion hormone- and neuroparsin-like peptides were identified from a variety of species, greatly expanding the number of known members of these families in crustaceans.
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Affiliation(s)
- Andrew E Christie
- Neuroscience Program, John W. and Jean C. Boylan Center for Cellular and Molecular Physiology, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, ME 04672, USA.
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Tagmount A, Wang M, Lindquist E, Tanaka Y, Teranishi KS, Sunagawa S, Wong M, Stillman JH. The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PLoS One 2010; 5:e9327. [PMID: 20174471 PMCID: PMC2824831 DOI: 10.1371/journal.pone.0009327] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 01/27/2010] [Indexed: 01/11/2023] Open
Abstract
Background With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings A set of ∼30K unique sequences (UniSeqs) representing ∼19K clusters were generated from ∼98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66% of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases. Conclusions/Significance The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.
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Affiliation(s)
- Abderrahmane Tagmount
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Erika Lindquist
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yoshihiro Tanaka
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America
| | - Kristen S. Teranishi
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America
| | - Shinichi Sunagawa
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Mike Wong
- Center for Computing in the Life Sciences, San Francisco State University, San Francisco, California, United States of America
| | - Jonathon H. Stillman
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Gard AL, Lenz PH, Shaw JR, Christie AE. Identification of putative peptide paracrines/hormones in the water flea Daphnia pulex (Crustacea; Branchiopoda; Cladocera) using transcriptomics and immunohistochemistry. Gen Comp Endocrinol 2009; 160:271-87. [PMID: 19135444 DOI: 10.1016/j.ygcen.2008.12.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 12/11/2008] [Accepted: 12/11/2008] [Indexed: 11/23/2022]
Abstract
The cladoceran crustacean Daphnia pulex has emerged as a model species for many biological fields, in particular environmental toxicology and toxicogenomics. Recently, this species has been the subject of an extensive transcriptome project, resulting in the generation and public deposition of over 150,000 expressed sequence tags (ESTs). This resource makes D. pulex an excellent model for protein discovery using bioinformatics. Here, in silico searches of the D. pulex EST database were conducted to identify transcripts encoding putative peptide precursors. Moreover, the mature peptides contained within the deduced prepro-hormones were predicted using online peptide processing programs and homology to known arthropod isoforms. In total, 63 putative peptide-encoding ESTs were identified encompassing 14 distinct peptide families/subfamilies: A-type allatostatin, B-type allatostatin, C-type allatostatin, bursicon (both alpha and beta subunit peptides), crustacean cardioactive peptide (CCAP), crustacean hyperglycemic hormone (CHH)/ion transport peptide (both CHH- and moult-inhibiting hormone-like subfamilies), diuretic hormone (calcitonin-like), ecdysis-triggering hormone (ETH), FMRFamide (both neuropeptide F and short neuropeptide F subfamilies), orcokinin and pigment dispersing hormone. From these transcripts, the structures of 76 full-length/partial peptides were predicted, which included the first C-type allatostatin-like peptide identified from a crustacean, the first crustacean calcitonin-like diuretic hormone, an undescribed CCAP isoform, two hitherto unknown ETH variants, and two new orcokinins. Neuronal localization of several of the identified peptide families was confirmed using immunohistochemitry (i.e. A-type allatostatin, CCAP, FMRFamide and PDH). In addition, immunohistochemical analyses identified other putative neuropeptides for which no ESTs had been found (i.e. corazonin, insect kinin, proctolin, red pigment concentrating hormone, SIFamide, sulfakinin and tachykinin-related peptide). Collectively, the data presented here not only catalog an extensive array of putative D. pulex peptide paracrines/hormones, but also provide a strong foundation for future investigations of the effects of environmental/anthropogenic stressors on peptidergic control in this model organism.
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Affiliation(s)
- Ashley L Gard
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
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