1
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Yagound B, West AJ, Richardson MF, Gruber J, Reid JG, Whiting MJ, Rollins LA. Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina). Mol Ecol 2022; 31:4949-4961. [PMID: 35894800 PMCID: PMC9804778 DOI: 10.1111/mec.16633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Andrea J. West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Mark F. Richardson
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia,Deakin Genomics Centre, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Jodie Gruber
- College of Life and Environmental SciencesUniversity of ExeterPenrynUK,School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Jack G. Reid
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Martin J. Whiting
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia,Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
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2
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Leung JYS, Zhang S, Connell SD. Is Ocean Acidification Really a Threat to Marine Calcifiers? A Systematic Review and Meta-Analysis of 980+ Studies Spanning Two Decades. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107407. [PMID: 35934837 DOI: 10.1002/smll.202107407] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Ocean acidification is considered detrimental to marine calcifiers, but mounting contradictory evidence suggests a need to revisit this concept. This systematic review and meta-analysis aim to critically re-evaluate the prevailing paradigm of negative effects of ocean acidification on calcifiers. Based on 5153 observations from 985 studies, many calcifiers (e.g., echinoderms, crustaceans, and cephalopods) are found to be tolerant to near-future ocean acidification (pH ≈ 7.8 by the year 2100), but coccolithophores, calcifying algae, and corals appear to be sensitive. Calcifiers are generally more sensitive at the larval stage than adult stage. Over 70% of the observations in growth and calcification are non-negative, implying the acclimation capacity of many calcifiers to ocean acidification. This capacity can be mediated by phenotypic plasticity (e.g., physiological, mineralogical, structural, and molecular adjustments), transgenerational plasticity, increased food availability, or species interactions. The results suggest that the impacts of ocean acidification on calcifiers are less deleterious than initially thought as their adaptability has been underestimated. Therefore, in the forthcoming era of ocean acidification research, it is advocated that studying how marine organisms persist is as important as studying how they perish, and that future hypotheses and experimental designs are not constrained within the paradigm of negative effects.
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Affiliation(s)
- Jonathan Y S Leung
- Faculty of Materials and Energy, Southwest University, Chongqing, 400715, P. R. China
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Sam Zhang
- Faculty of Materials and Energy, Southwest University, Chongqing, 400715, P. R. China
| | - Sean D Connell
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
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3
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Wall-Palmer D, Mekkes L, Ramos-Silva P, Dämmer LK, Goetze E, Bakker K, Duijm E, Peijnenburg KTCA. The impacts of past, present and future ocean chemistry on predatory planktonic snails. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202265. [PMID: 34386247 PMCID: PMC8334855 DOI: 10.1098/rsos.202265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
The atlantid heteropods represent the only predatory, aragonite shelled zooplankton. Atlantid shell production is likely to be sensitive to ocean acidification (OA), and yet we know little about their mechanisms of calcification, or their response to changing ocean chemistry. Here, we present the first study into calcification and gene expression effects of short-term OA exposure on juvenile atlantids across three pH scenarios: mid-1960s, ambient and 2050 conditions. Calcification and gene expression indicate a distinct response to each treatment. Shell extension and shell volume were reduced from the mid-1960s to ambient conditions, suggesting that calcification is already limited in today's South Atlantic. However, shell extension increased from ambient to 2050 conditions. Genes involved in protein synthesis were consistently upregulated, whereas genes involved in organismal development were downregulated with decreasing pH. Biomineralization genes were upregulated in the mid-1960s and 2050 conditions, suggesting that any deviation from ambient carbonate chemistry causes stress, resulting in rapid shell growth. We conclude that atlantid calcification is likely to be negatively affected by future OA. However, we also found that plentiful food increased shell extension and shell thickness, and so synergistic factors are likely to impact the resilience of atlantids in an acidifying ocean.
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Affiliation(s)
- Deborah Wall-Palmer
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Lisette Mekkes
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Paula Ramos-Silva
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Linda K. Dämmer
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
- Environmental Geology, Department of Geology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Erica Goetze
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Karel Bakker
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Elza Duijm
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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4
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López-Landavery EA, Carpizo-Ituarte EJ, Pérez-Carrasco L, Díaz F, la Cruz FLD, García-Esquivel Z, Hernández-Ayón JM, Galindo-Sánchez CE. Acidification stress effect on umbonate veliger larval development in Panopea globosa. MARINE POLLUTION BULLETIN 2021; 163:111945. [PMID: 33444999 DOI: 10.1016/j.marpolbul.2020.111945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Ocean acidification generates a decrease in calcium carbonate availability essential for biomineralization in organisms such as mollusks. This effect was evaluated on Panopea globosa exposing for 7 days umbonate veliger larvae to two pH treatments: experimental (pH 7.5) and control (pH 8.0). Exposure to pH 7.5 affected growth, reducing larval shell length from 5.15-13.34% compared to the control group. This size reduction was confirmed with electron microscopy, also showing shell damage. The physiological response showed an increase in oxygen consumption in larvae exposed to low pH with a maximum difference of 1.57 nmol O2 h-1 larvae-1 at day 7. The gene expression analyses reported high expression values for nicotinamide adenine dinucleotide (NADH) dehydrogenase and Perlucin in larvae at pH 7.5, suggesting a higher energetic cost in this larval group to maintain homeostasis. In conclusion, this study showed that acidification affected development of P. globosa umbonate veliger larvae.
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Affiliation(s)
- Edgar A López-Landavery
- Laboratorio de Genómica Funcional, Departmento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, B.C, Mexico
| | - Eugenio J Carpizo-Ituarte
- Laboratorio de Ecología y Biología del Desarrollo, Universidad Autónoma de Baja California (UABC), Carretera Tijuana-Ensenada No. 3917, Ensenada, B.C, Mexico
| | - Leonel Pérez-Carrasco
- Laboratorio de Genómica Funcional, Departmento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, B.C, Mexico
| | - Fernando Díaz
- Laboratorio de Genómica Funcional, Departmento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, B.C, Mexico
| | - Fabiola Lafarga-De la Cruz
- Departamento de Acuicultura, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, B.C, Mexico
| | - Zaul García-Esquivel
- Laboratorio de Biotecnología de Moluscos, Universidad Autónoma de Baja California (UABC), Carretera Tijuana-Ensenada No. 3917, Ensenada, B.C, Mexico
| | - José M Hernández-Ayón
- Laboratorio de Biogeoquímica Marina, Universidad Autónoma de Baja California (UABC), Carretera Tijuana-Ensenada No. 3917, Ensenada, B.C, Mexico
| | - Clara E Galindo-Sánchez
- Laboratorio de Genómica Funcional, Departmento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, B.C, Mexico.
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5
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Mekkes L, Renema W, Bednaršek N, Alin SR, Feely RA, Huisman J, Roessingh P, Peijnenburg KTCA. Pteropods make thinner shells in the upwelling region of the California Current Ecosystem. Sci Rep 2021; 11:1731. [PMID: 33462349 PMCID: PMC7814018 DOI: 10.1038/s41598-021-81131-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/29/2020] [Indexed: 01/29/2023] Open
Abstract
Shelled pteropods are widely regarded as bioindicators for ocean acidification, because their fragile aragonite shells are susceptible to increasing ocean acidity. While short-term incubations have demonstrated that pteropod calcification is negatively impacted by ocean acidification, we know little about net calcification in response to varying ocean conditions in natural populations. Here, we examine in situ calcification of Limacina helicina pteropods collected from the California Current Ecosystem, a coastal upwelling system with strong spatial gradients in ocean carbonate chemistry, dissolved oxygen and temperature. Depth-averaged pH ranged from 8.03 in warmer offshore waters to 7.77 in cold CO2-rich waters nearshore. Based on high-resolution micro-CT technology, we showed that shell thickness declined by ~ 37% along the upwelling gradient from offshore to nearshore water. Dissolution marks covered only ~ 2% of the shell surface area and were not associated with the observed variation in shell thickness. We thus infer that pteropods make thinner shells where upwelling brings more acidified and colder waters to the surface. Probably the thinner shells do not result from enhanced dissolution, but are due to a decline in calcification. Reduced calcification of pteropods is likely to have major ecological and biogeochemical implications for the cycling of calcium carbonate in the oceans.
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Affiliation(s)
- Lisette Mekkes
- grid.425948.60000 0001 2159 802XNaturalis Biodiversity Center, Leiden, The Netherlands ,grid.7177.60000000084992262Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem Renema
- grid.425948.60000 0001 2159 802XNaturalis Biodiversity Center, Leiden, The Netherlands ,grid.7177.60000000084992262Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nina Bednaršek
- grid.419399.f0000 0001 0057 0239Southern California Coastal Water Research Project, Costa Mesa, CA USA ,grid.419523.80000 0004 0637 0790National Institute of Biology, Ljubljana, 1000 Slovenia
| | - Simone R. Alin
- grid.3532.70000 0001 1266 2261Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, WA USA
| | - Richard A. Feely
- grid.3532.70000 0001 1266 2261Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, WA USA
| | - Jef Huisman
- grid.7177.60000000084992262Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Roessingh
- grid.7177.60000000084992262Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Katja T. C. A. Peijnenburg
- grid.425948.60000 0001 2159 802XNaturalis Biodiversity Center, Leiden, The Netherlands ,grid.7177.60000000084992262Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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6
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Choo LQ, Bal TMP, Goetze E, Peijnenburg KTCA. Oceanic dispersal barriers in a holoplanktonic gastropod. J Evol Biol 2021; 34:224-240. [PMID: 33150701 PMCID: PMC7894488 DOI: 10.1111/jeb.13735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large-scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI ΦST = 0.230, 28S ΦST = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise ΦST comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.
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Affiliation(s)
- Le Qin Choo
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Thijs M. P. Bal
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Erica Goetze
- Department of OceanographyUniversity of Hawaiʻi at MānoaHonoluluUSA
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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7
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Devens HR, Davidson PL, Deaker DJ, Smith KE, Wray GA, Byrne M. Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma. Mol Ecol 2020; 29:4618-4636. [PMID: 33002253 PMCID: PMC8994206 DOI: 10.1111/mec.15664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 09/01/2023]
Abstract
Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyse gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and much smaller than genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.
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Affiliation(s)
| | | | - Dione J Deaker
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Kathryn E Smith
- The Laboratory, The Marine Biological Association, Plymouth, UK
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Maria Byrne
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
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8
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Peijnenburg KTCA, Janssen AW, Wall-Palmer D, Goetze E, Maas AE, Todd JA, Marlétaz F. The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle. Proc Natl Acad Sci U S A 2020; 117:25609-25617. [PMID: 32973093 PMCID: PMC7568333 DOI: 10.1073/pnas.1920918117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pteropods are a group of planktonic gastropods that are widely regarded as biological indicators for assessing the impacts of ocean acidification. Their aragonitic shells are highly sensitive to acute changes in ocean chemistry. However, to gain insight into their potential to adapt to current climate change, we need to accurately reconstruct their evolutionary history and assess their responses to past changes in the Earth's carbon cycle. Here, we resolve the phylogeny and timing of pteropod evolution with a phylogenomic dataset (2,654 genes) incorporating new data for 21 pteropod species and revised fossil evidence. In agreement with traditional taxonomy, we recovered molecular support for a division between "sea butterflies" (Thecosomata; mucus-web feeders) and "sea angels" (Gymnosomata; active predators). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled, and unshelled groups, diverged in the mid- to late Cretaceous. Hence, these clades originated prior to and subsequently survived major global change events, including the Paleocene-Eocene Thermal Maximum (PETM), the closest analog to modern-day ocean acidification and warming. Our findings indicate that planktonic aragonitic calcifiers have shown resilience to perturbations in the Earth's carbon cycle over evolutionary timescales.
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Affiliation(s)
- Katja T C A Peijnenburg
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands;
- Department Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Arie W Janssen
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands
| | - Deborah Wall-Palmer
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands
| | - Erica Goetze
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI 96822
| | - Amy E Maas
- Bermuda Institute of Ocean Sciences, St. Georges GE01, Bermuda
| | - Jonathan A Todd
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna-son 904-0495, Japan
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9
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Abstract
Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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10
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Strader ME, Wong JM, Hofmann GE. Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey. Front Zool 2020; 17:7. [PMID: 32095155 PMCID: PMC7027112 DOI: 10.1186/s12983-020-0350-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/06/2020] [Indexed: 01/16/2023] Open
Abstract
For nearly a decade, the metazoan-focused research community has explored the impacts of ocean acidification (OA) on marine animals, noting that changes in ocean chemistry can impact calcification, metabolism, acid-base regulation, stress response and behavior in organisms that hold high ecological and economic value. Because OA interacts with several key physiological processes in marine organisms, transcriptomics has become a widely-used method to characterize whole organism responses on a molecular level as well as inform mechanisms that explain changes in phenotypes observed in response to OA. In the past decade, there has been a notable rise in studies that examine transcriptomic responses to OA in marine metazoans, and here we attempt to summarize key findings across these studies. We find that organisms vary dramatically in their transcriptomic responses to pH although common patterns are often observed, including shifts in acid-base ion regulation, metabolic processes, calcification and stress response mechanisms. We also see a rise in transcriptomic studies examining organismal response to OA in a multi-stressor context, often reporting synergistic effects of OA and temperature. In addition, there is an increase in studies that use transcriptomics to examine the evolutionary potential of organisms to adapt to OA conditions in the future through population and transgenerational experiments. Overall, the literature reveals complex organismal responses to OA, in which some organisms will face more dramatic consequences than others. This will have wide-reaching impacts on ocean communities and ecosystems as a whole.
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Affiliation(s)
- Marie E Strader
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA.,2Department of Biological Sciences, Auburn University, Auburn, AL 36849 USA
| | - Juliet M Wong
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA.,3Present address: Department of Biological Sciences, Florida International University, North Miami, FL 33181 USA
| | - Gretchen E Hofmann
- 1Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106 USA
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11
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Melzner F, Mark FC, Seibel BA, Tomanek L. Ocean Acidification and Coastal Marine Invertebrates: Tracking CO 2 Effects from Seawater to the Cell. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:499-523. [PMID: 31451083 DOI: 10.1146/annurev-marine-010419-010658] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the last few decades, numerous studies have investigated the impacts of simulated ocean acidification on marine species and communities, particularly those inhabiting dynamic coastal systems. Despite these research efforts, there are many gaps in our understanding, particularly with respect to physiological mechanisms that lead to pathologies. In this review, we trace how carbonate system disturbances propagate from the coastal environment into marine invertebrates and highlight mechanistic links between these disturbances and organism function. We also point toward several processes related to basic invertebrate biology that are severely understudied and prevent an accurate understanding of how carbonate system dynamics influence organismic homeostasis and fitness-related traits. We recommend that significant research effort be directed to studying cellular phenotypes of invertebrates acclimated or adapted to elevated seawater pCO2 using biochemical and physiological methods.
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Affiliation(s)
- Frank Melzner
- Marine Ecology Research Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany;
| | - Felix C Mark
- Department of Integrative Ecophysiology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Brad A Seibel
- College of Marine Science, University of South Florida, St. Petersburg, Florida 33701, USA;
| | - Lars Tomanek
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California 93407, USA;
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Choo LQ, Bal TMP, Choquet M, Smolina I, Ramos-Silva P, Marlétaz F, Kopp M, Hoarau G, Peijnenburg KTCA. Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance. BMC Genomics 2020; 21:11. [PMID: 31900119 PMCID: PMC6942316 DOI: 10.1186/s12864-019-6372-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. RESULTS We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. CONCLUSION The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.
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Affiliation(s)
- Le Qin Choo
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| | - Thijs M P Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Paula Ramos-Silva
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Katja T C A Peijnenburg
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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