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Choi TJ, Malik A, Han SM, Kim CB. Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones. BMC Genomics 2024; 25:725. [PMID: 39060996 PMCID: PMC11282837 DOI: 10.1186/s12864-024-10643-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress. RESULTS KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype. CONCLUSIONS Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.
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Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Korea
| | - Seung-Min Han
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea.
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2
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Jin Q, Wang Y, Zhang K, Li G, Chen Y, Hong Y, Cheng H, Deng D. Morphological and life-history trait plasticity of two Daphnia species induced by fish kairomones. Ecol Evol 2024; 14:e11422. [PMID: 38846709 PMCID: PMC11154820 DOI: 10.1002/ece3.11422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/15/2024] [Accepted: 05/03/2024] [Indexed: 06/09/2024] Open
Abstract
Daphnia can avoid predation by sensing fish kairomones and producing inducible defenses by altering the phenotype. In this study, the results showed that the morphological and life-history strategies of two Daphnia species (Daphnia pulex and Daphnia sinensis) exposed to Aristichthys nobilis kairomones. In the presence of fish kairomones, the two Daphnia species exhibited significantly smaller body length at maturity, smaller body length of offspring at the 10th instar, and longer relative tail spine of offspring. Nevertheless, other morphological and life-history traits of the two Daphnia species differed. D. pulex showed a significantly longer relative tail spine length and earlier age at maturity after exposure to fish kairomones. The total offspring number of D. sinensis exposed to fish kairomones was significantly higher than that of the control group, whereas that of D. pulex was significantly lower. These results suggest that the two Daphnia species have different inducible defense strategies (e.g., morphological and life-history traits) during prolonged exposure to A. nobilis kairomones, and their offspring also develop morphological defenses to avoid predation. It will provide reference for further exploring the adaptive evolution of Daphnia morphology and life-history traits in the presence of planktivorous fish.
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Affiliation(s)
- Qide Jin
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Yeping Wang
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Kun Zhang
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Guoqing Li
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Yanan Chen
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Yujuan Hong
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Hanxue Cheng
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
| | - Daogui Deng
- School of Life SciencesHuaibei Normal UniversityHuaibeiAnhuiChina
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3
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Baludo MY, Octorina P, Beckerman A, Straile D. Antipredator responses of three Daphnia species within the D. longispina species complex to two invertebrate predators. Ecol Evol 2024; 14:e10841. [PMID: 38205375 PMCID: PMC10776305 DOI: 10.1002/ece3.10841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Prey communities in natural environments face a diverse array of predators with distinct hunting techniques. However, most studies have focused only on the interactions between a single prey species and one or more predators and typically only one of many induced defense traits, which limits our understanding of the broader effects of predators on prey communities. In this study, we conducted a common garden experiment using five clones each of three Daphnia species (D. cucullata, D. galeata, and D. longispina) from the D. longispina species complex to investigate the plasticity of predator-induced defenses in response to two predators in a community ecology setting. Five clones from each species were subjected to predator kairomones from two closely related invertebrate predators that are common in several European lakes, Bythotrephes longimanus or Leptodora kindtii for a duration of 10 days, and the morphological traits of body size, head size, spina size, and the presence of spinules on the ventral and dorsal carapace margins were measured. We show that among the species within this species complex there are different antipredator reactions to the invertebrate predators. The induced responses exhibited were species, trait, and predator-specific. Notably, D. galeata and D. cucullata developed distinctive helmets as defensive mechanisms, while microdefenses were induced in D. galeata and D. longispina, but not in D. cucullata. This demonstrates that the expression of micro- and macrodefenses across species was unrelated, highlighting the possible independent evolution of microstructures as defensive modules in Daphnia's antipredator strategies. This study is the first to document both micro- and macrodefensive phenotypic plasticity in three co-occurring Daphnia species within the D. longispina species complex. The differences in inducible defenses may have a substantial impact on how these three species cohabit with Bythotrephes and Leptodora.
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Affiliation(s)
| | - Pelita Octorina
- Limnologisches InstitutUniversität KonstanzKonstanzGermany
- Department AquacultureMuhammadiyah University of SukabumiSukabumiIndonesia
| | - Andrew Beckerman
- School of Biosciences, Ecology and Evolutionary BiologyUniversity of SheffieldSheffieldUK
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Augustyniak M, Kołacka K, Kobak J, Hliwa P, Kłosiński P, Poznańska-Kakareko M, Jermacz Ł, Kakareko T. Differences in predator-avoidance behavior between two invasive gobies and their native competitors. Curr Zool 2023; 69:727-737. [PMID: 37876643 PMCID: PMC10591152 DOI: 10.1093/cz/zoac082] [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: 05/18/2022] [Accepted: 10/07/2022] [Indexed: 10/26/2023] Open
Abstract
Globally, fish are frequently introduced beyond their native range. Some, like Ponto-Caspian gobies, are becoming invasive, achieving high colonization rates and constituting frequent prey for native predators. However, little is known about the effectiveness of antipredator behaviors of the invaders, which may shape their role in the invaded community and contribute to the invasion success. We compared antipredator behaviors of invasive gobies and native fish species after their detection by the predator, when the danger becomes direct. We studied 2 fish pairs, each consisting of an invasive and native species co-occurring in the environment and belonging to the same prey guild: (1) the racer goby Babka gymnotrachelus versus European bullhead Cottus gobio, (2) the monkey goby Neogobius fluviatilis versus gudgeon Gobio gobio, facing a naïve predator (the Eurasian perch Perca fluviatilis). We analyzed behaviors of single prey individuals (escaping, staying in shelter, and activity) and single predators (activity, searching, following, capturing, and latency to prey consumption). In the predator presence, the bullhead was less active and more often managed to escape after capture than the racer goby. The gudgeon escaped before the capture more often than the monkey goby. The predator succeeded later with the bullhead compared to racer goby, whereas no differences in ingestion time occurred between the gudgeon and monkey goby. The results suggest that, in terms of hunting effort of native predators, the invasive gobies are equivalent to or more profitable prey than their native analogs, which can facilitate the integration of the gobies into local food webs.
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Affiliation(s)
- Mateusz Augustyniak
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Kalina Kołacka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Jarosław Kobak
- Department of Invertebrate Zoology and Parasitology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Piotr Hliwa
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury, Oczapowskiego 5, 10-719, Olsztyn, Poland
| | - Piotr Kłosiński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Małgorzata Poznańska-Kakareko
- Department of Invertebrate Zoology and Parasitology, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Łukasz Jermacz
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Tomasz Kakareko
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
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5
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Choi TJ, Han SM, Malik A, Kim CB. Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea. BMC Genomics 2023; 24:580. [PMID: 37784038 PMCID: PMC10544471 DOI: 10.1186/s12864-023-09701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Phenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustacean Daphnia galeata is a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two Korean Daphnia galeata genotypes, KE1, and KB11, collected in the same environment. RESULTS When exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1. CONCLUSIONS The current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two Korean D. galeata genotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.
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Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Seung-Min Han
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Republic of Korea.
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6
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Werner C, Otte KA, von Elert E. Phenotypic convergence in a natural Daphnia population acclimated to low temperature. Ecol Evol 2021; 11:15312-15324. [PMID: 34765180 PMCID: PMC8571613 DOI: 10.1002/ece3.8217] [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: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 11/08/2022] Open
Abstract
Fluidity of a given membrane decreases at lower ambient temperatures, whereas it rises at increasing temperatures, which is achieved through changes in membrane lipid composition. In consistence with homeoviscous adaptation theory, lower temperatures result in increased tissue concentrations of polyunsaturated fatty acids (PUFAs) in Daphnia magna, suggesting a higher PUFA requirement at lower temperatures. However, so far homeoviscous adaptation has been suggested for single or geographically separated Daphnia genotypes only. Here, we investigated changes in relative fatty acid (FA) tissue concentrations in response to a lower temperature (15°C) within a D. magna population. We determined juvenile growth rates (JGR) and FA patterns of 14 genotypes that were grown on Chlamydomonas klinobasis at 15°C and 20°C. We report significant differences of JGR and the relative body content of various FAs between genotypes at either temperature and between temperatures. Based on slopes of reaction norms, we found genotype-specific changes in FA profiles between temperatures suggesting that genotypes have different strategies to cope with changing temperatures. In a hierarchical clustering analysis, we grouped genotypes according to differences in direction and magnitude of changes in relative FA content, which resulted in three clusters of genotypes following different patterns of changes in FA composition. These patterns suggest a lower importance of the PUFA eicosapentaenoic acid (EPA, C20:5ω3) than previously assumed. We calculated an unsaturation index (UI) as a proxy for membrane fluidity at 15°C, and we neither found significant differences for this UI nor for fitness, measured as JGR, between the three genotype clusters. We conclude that these three genotype clusters represent different physiological solutions to temperature changes by altering the relative share of different FAs, but that their phenotypes converge with respect to membrane fluidity and JGR. These clusters will be subjected to different degrees of PUFA limitation when sharing the same diet.
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Affiliation(s)
- Christian Werner
- Aquatic Chemical EcologyInstitute for ZoologyUniversity of CologneKölnGermany
| | - Kathrin A. Otte
- Aquatic Chemical EcologyInstitute for ZoologyUniversity of CologneKölnGermany
| | - Eric von Elert
- Aquatic Chemical EcologyInstitute for ZoologyUniversity of CologneKölnGermany
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7
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Schwarzenberger A, Ilić M, Von Elert E. Daphnia populations are similar but not identical in tolerance to different protease inhibitors. HARMFUL ALGAE 2021; 106:102062. [PMID: 34154785 DOI: 10.1016/j.hal.2021.102062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/06/2021] [Accepted: 05/30/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial blooms often produce different classes and chemical variants of toxins such as dietary protease inhibitors (PIs) that affect the keystone grazer Daphnia. However, it has been shown that Daphnia populations are able to locally adapt to frequently occurring dietary PIs by modulating their digestive proteases. Up until now, local adaptation has exclusively been tested by making use of single cyanobacterial strains and by measuring average population tolerance. In contrast, we measured juvenile somatic growth rates and egg numbers of several individual clones per each of three different D. magna populations that have previously been found to be either tolerant or sensitive to the Microcystis strain BM25. Clones from the three D. magna populations were either treated with BM25 that produces three different protease inhibitor variants of the class of Ahp-cyclodepsipeptides or another Microcystis strain that produces two other Ahp-cyclodepsipeptide variants. Subsequently, the population growth was calculated as mean of the single-clone growth rates. Both tolerant populations (which originate from ponds with a cyanobacterial history) proved to be similarly tolerant to both Microcystis strains. However, single genotypes of the populations differed in their response to the different strains. Both the tolerant and the sensitive populations contained both sensitive and tolerant genotypes but in different proportions. Furthermore, the genotypes from the sensitive population showed a higher variance in response to one or both strains. Trade-offs between somatic growth rate and clutch size were found in one of the tolerant populations that originated from a pond where cyanobacteria were frequent in the past but completely absent since the pond's restoration. Because of those intra-population difference, we conclude that the tolerant populations were putatively selected by different Ahp-cyclodepsipeptide variants in the past and that all populations still possess the potential to adapt to other environmental conditions by genotype frequency shifts.
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Affiliation(s)
- Anke Schwarzenberger
- University of Konstanz, Limnological Institute, Mainaustraße 252, 78464 Konstanz, Germany.
| | - Maja Ilić
- Queen's University Belfast, School of Biological Sciences, 19 Chlorine Gardens, BT9 5DL Belfast, United Kingdom
| | - Eric Von Elert
- University of Cologne, Institute for Zoology, Zülpicherstraße 47b, 50674 Cologne, Germany
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8
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Lu N, Sun Y, Wei J, Gu L, Zhang L, Yang Z, Huang Y. Toxic Microcystis aeruginosa alters the resource allocation in Daphnia mitsukuri responding to fish predation cues. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116918. [PMID: 33743270 DOI: 10.1016/j.envpol.2021.116918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/27/2021] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Many prey organisms adaptively respond to predation risk by inducible defenses with underlying tradeoffs in resource allocation. Cyanobacterial blooms expose zooplankton to poor food conditions, affecting the herbivores' fitness. Given the interferences on resources allocation and life history traits, poor-quality cyanobacteria are predicted to affect the adaptive predator-induced responses in zooplankton. Here, we exposed two clones (i.e., clones SH and ZJ) of the cladoceran Daphnia mitsukuri to different combinations of fish predation cues and diets containing toxic Microcystis aeruginosa (0%-30%). D. mitsukuri matured at a small size and had elongated relative tail spine as adaptive responses to fish cues. Despite the comparable tail spine defense, fish cue-induced changes in growth and reproduction in the clone SH were more pronounced than those in the clone ZJ under no M. aeruginosa. Animals accumulated microcystin in the whole body with increasing abundance of M. aeruginosa. However, the inducible enhanced tail spine allometry was not affected, resulting in unchanged tail spine defense by Daphnia under all M. aeruginosa treatments. By contrast, M. aeruginosa remarkably decreased the adaptive maturation size and the offspring number in all animals. However, the inducible reproductive effort tended to increase or remain unchanged depending on clones associated with the constant or decreased responses of the somatic growth effort under increasing M. aeruginosa. Our results suggested that toxic M. aeruginosa did not alter the resource allocation to antipredator morphological defense but affected the somatic growth and reproduction in D. mitsukuri under fish cues. The present study highlights the different effects of toxic cyanobacteria on adaptive predator-induced responses in zooplankton, promoting the understanding for the morphological defense-mediated predator-prey interactions in eutrophic environments.
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Affiliation(s)
- Na Lu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Yunfei Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Junjun Wei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Lei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
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Pötter L, Krebs N, Horstmann M, Tollrian R, Weiss LC. Long-term effects of elevated pCO 2 levels on the expression of Chaoborus-induced defences in Daphnia pulex. ZOOLOGY 2021; 146:125909. [PMID: 33780896 DOI: 10.1016/j.zool.2021.125909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Increased carbon dioxide from fossil fuel combustion results in an enrichment of CO2 in the global carbon cycle. Recent evidence indicates that rising atmospheric CO2 impacts the partial pressure of carbon dioxide (pCO2) in freshwaters. This affects freshwater biota by disrupting chemical communication between predator and prey. One such well-described predator-prey interaction is the phantom midge larva Chaoborus preying on the freshwater crustacean Daphnia pulex. To counter Chaoborus predation, D. pulex develops defensive neckteeth in response to chemical cues. The strength of neckteeth expression is reduced when D. pulex experience elevated pCO2 levels. This is discussed to directly impair predator perception and results in reduced defence expression. However, it is not known whether there are also long-term effects associated with continuous elevated pCO2. Here, we investigated the effect of long-term exposure of D. pulex to elevated pCO2 levels in a life-table experiment over three generations. Using a flow-through system, we continuously exposed D. pulex to cues released by the predatory larva Chaoborus and control or elevated pCO2 levels. We determined morphological defence expression in the 2nd juvenile instar and the number of neonates as a measure for life-history traits over three successive generations. We detected that elevated pCO2 significantly reduces the expression of predator-induced morphological defences (i.e. neckteeth) and life-history parameters (i.e. number of neonates) in successive generations. Our data clearly show that at least three generations become more vulnerable to predation without indications of transgenerational acclimation. As Daphnia is a keystone grazer of freshwater ecosystems, this may destabilise population growth rates. In conclusion, long-term effects of pCO2-induced reduction of predator-induced plasticity may significantly affect trophic interactions.
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Affiliation(s)
- Leonie Pötter
- Department of Animal Ecology, Evolution & Biodiversity, Ruhr-University Bochum, NDEF, Universitaetsstraße 150, D-44780 Bochum, Germany.
| | - Nina Krebs
- Department of Animal Ecology, Evolution & Biodiversity, Ruhr-University Bochum, NDEF, Universitaetsstraße 150, D-44780 Bochum, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Department for Integrative Ecophysiology, Am Handelshafen 12, E-1555, 27570 Bremerhaven, Germany.
| | - Martin Horstmann
- Department of Animal Ecology, Evolution & Biodiversity, Ruhr-University Bochum, NDEF, Universitaetsstraße 150, D-44780 Bochum, Germany.
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution & Biodiversity, Ruhr-University Bochum, NDEF, Universitaetsstraße 150, D-44780 Bochum, Germany.
| | - Linda C Weiss
- Department of Animal Ecology, Evolution & Biodiversity, Ruhr-University Bochum, NDEF, Universitaetsstraße 150, D-44780 Bochum, Germany.
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10
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Tams V, Nickel JH, Ehring A, Cordellier M. Insights into the genetic basis of predator-induced response in Daphnia galeata. Ecol Evol 2020; 10:13095-13108. [PMID: 33304520 PMCID: PMC7713943 DOI: 10.1002/ece3.6899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges-these responses comprise morphological, behavioral but also life-history changes. Alteration of life-history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia. However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator-induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator-induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D. galeata. Furthermore, we used an orthology-based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator-induced responses in Daphnia. Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones-mediated life-history changes in other Daphnia species.
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Affiliation(s)
- Verena Tams
- Institute of Marine Ecosystem and Fishery ScienceUniversität HamburgHamburgGermany
| | | | - Anne Ehring
- Institute of ZoologyUniversität HamburgHamburgGermany
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11
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Ravindran SP, Tams V, Cordellier M. Transcriptome‐wide genotype–phenotype associations in
Daphnia
in a predation risk environment. J Evol Biol 2020; 34:879-892. [DOI: 10.1111/jeb.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/03/2020] [Accepted: 08/29/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Suda Parimala Ravindran
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Verena Tams
- Institute of Marine Ecosystem and Fishery Science Universität Hamburg Hamburg Germany
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Suresh S, Crease TJ, Cristescu ME, Chain FJJ. Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure. BMC Genomics 2020; 21:433. [PMID: 32586292 PMCID: PMC7318467 DOI: 10.1186/s12864-020-06831-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. RESULTS By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. CONCLUSIONS Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
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Affiliation(s)
- Sneha Suresh
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- Present address: The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong SAR
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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Abstract
Phenotypic plasticity in defensive traits is an appropriate mechanism to cope with the variable hazard of a frequently changing predator spectrum. In the animal kingdom these so-called inducible defences cover the entire taxonomic range from protozoans to vertebrates. The inducible defensive traits range from behaviour, morphology, and life-history adaptations to the activation of specific immune systems in vertebrates. Inducible defences in prey species play important roles in the dynamics and functioning of food webs. Freshwater zooplankton show the most prominent examples of inducible defences triggered by chemical cues, so-called kairomones, released by predatory invertebrates and fish. The objective of this review is to highlight recent progress in research on inducible defences in freshwater zooplankton concerning behaviour, morphology, and life-history, as well as difficulties of studies conducted in a multipredator set up. Furthermore, we outline costs associated with the defences and discuss difficulties as well as the progress made in characterizing defence-inducing cues. Finally, we aim to indicate further possible routes in this field of research and provide a comprehensive table of inducible defences with respect to both prey and predator species.
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Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
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Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
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