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Sanna D, Azzena I, Locci C, Ankon P, Kružić P, Manfrin C, Pallavicini A, Ciriaco S, Segarich M, Batistini E, Scarpa F, Casu M. Reconstructing the Evolutionary History of Pinna nobilis: New Genetic Signals from the Past of a Species on the Brink of Extinction. Animals (Basel) 2023; 14:114. [PMID: 38200845 PMCID: PMC10778441 DOI: 10.3390/ani14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Pinna nobilis, commonly known as the noble pen shell, is a marine bivalve endemic to the Mediterranean Sea. Unfortunately, due to a multifactorial disease that began affecting its populations in 2016, the species is currently facing the threat of extinction. To gain insights into the evolutionary history of P. nobilis before the mass mortality event (MME), and to obtain a comprehensive understanding of how evolutionary processes led to the adaptation of the species into the Mediterranean Sea, phylogenetic and phylogeographic analyses were carried out. The dataset analysed includes 469 sequences of COI gene fragment both from GenBank and the present study (100). The analysis performed evidenced that P. nobilis diverged about 2.5 mya, after the entrance of its ancestor into the Mediterranean Sea following the Zanclean flood (5.33 mya). Moreover, our results suggest that the starting point of colonisation was the central part of the western Mediterranean basin, with the eastern basin being populated subsequently. From a conservational viewpoint, these results provide important hints for present and future restocking plans, helping to reconstruct the pre-existing genetic variability in sites where the species became extinct.
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Affiliation(s)
- Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Ilenia Azzena
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Chiara Locci
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
| | - Pavel Ankon
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (P.A.); (P.K.)
| | - Petar Kružić
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (P.A.); (P.K.)
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy; (C.M.); (A.P.)
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste, Italy; (C.M.); (A.P.)
| | - Saul Ciriaco
- WWF AMP Miramare, Via Beirut 2/4, 34151 Trieste, Italy;
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Marco Segarich
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Edoardo Batistini
- Shoreline Soc. Coop., AREA Science Park, Padriciano 99, 34149 Trieste, Italy; (M.S.); (E.B.)
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (I.A.); (C.L.); (F.S.)
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
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Cerini F, Childs DZ, Clements CF. A predictive timeline of wildlife population collapse. Nat Ecol Evol 2023; 7:320-331. [PMID: 36702859 DOI: 10.1038/s41559-023-01985-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023]
Abstract
Contemporary rates of biodiversity decline emphasize the need for reliable ecological forecasting, but current methods vary in their ability to predict the declines of real-world populations. Acknowledging that stressor effects start at the individual level, and that it is the sum of these individual-level effects that drives populations to collapse, shifts the focus of predictive ecology away from using predominantly abundance data. Doing so opens new opportunities to develop predictive frameworks that utilize increasingly available multi-dimensional data, which have previously been overlooked for ecological forecasting. Here, we propose that stressed populations will exhibit a predictable sequence of observable changes through time: changes in individuals' behaviour will occur as the first sign of increasing stress, followed by changes in fitness-related morphological traits, shifts in the dynamics (for example, birth rates) of populations and finally abundance declines. We discuss how monitoring the sequential appearance of these signals may allow us to discern whether a population is increasingly at risk of collapse, or is adapting in the face of environmental change, providing a conceptual framework to develop new forecasting methods that combine multi-dimensional (for example, behaviour, morphology, life history and abundance) data.
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Affiliation(s)
- Francesco Cerini
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Dylan Z Childs
- School of Biosciences, University of Sheffield, Sheffield, UK
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Dong S, Liu D, Zhu B, Yu L, Shan H, Wang F. A Dynamic Energy Budget Model for Kuruma Shrimp Penaeus japonicus: Parameterization and Application in Integrated Marine Pond Aquaculture. Animals (Basel) 2022; 12:ani12141828. [PMID: 35883375 PMCID: PMC9311514 DOI: 10.3390/ani12141828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
Individual growth models can form the basis of population dynamics assessment and ecosystem model construction. In order to provide a basic module for an ecosystem model of an integrated marine aquaculture pond, an individual growth model was constructed for kuruma shrimp (Penaeus japonicus) based on dynamic energy budget (DEB) theory. The model was first parameterized based on a covariation method using the Add-my-Pet (AmP) procedure. The parametric estimation model underestimated the ultimate abdominal length for female shrimp, and the predicted values of other zero-variate parameters were generally consistent with observed values. The relative errors of the predicted and observed values of the univariate data set within three geographical regions showed acceptable goodness of fit. Parameter estimation achieved an overall goodness of fit with a mean relative error of 0.048 and a symmetric mean squared error of 0.066. A DEB model was constructed using the estimated parameters, and the goodness-of-fit indicators (R square, mean bias and absolute and relative root mean square error) showed that the model was able to reproduce the growth of kuruma shrimp in terms of total length and wet weight with high accuracy. The results provide data to support the subsequent development of integrated aquaculture management at the ecosystem level.
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Affiliation(s)
- Shipeng Dong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266003, China
| | - Dapeng Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266003, China
| | - Boshan Zhu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266003, China
| | - Liye Yu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266003, China
| | - Hongwei Shan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
| | - Fang Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (S.D.); (D.L.); (B.Z.); (L.Y.); (H.S.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266003, China
- Correspondence:
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Pousse É, Munroe D, Hart D, Hennen D, Cameron LP, Rheuban JE, Wang ZA, Wikfors GH, Meseck SL. Dynamic energy budget modeling of Atlantic surfclam, Spisula solidissima, under future ocean acidification and warming. MARINE ENVIRONMENTAL RESEARCH 2022; 177:105602. [PMID: 35462229 DOI: 10.1016/j.marenvres.2022.105602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/03/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
A dynamic energy budget (DEB) model integrating pCO2 was used to describe ocean acidification (OA) effects on Atlantic surfclam, Spisula solidissima, bioenergetics. Effects of elevated pCO2 on ingestion and somatic maintenance costs were simulated, validated, and adapted in the DEB model based upon growth and biological rates acquired during a 12-week laboratory experiment. Temperature and pCO2 were projected for the next 100 years following the intergovernmental panel on climate change representative concentration pathways scenarios (2.6, 6.0, and 8.5) and used as forcing variables to project surfclam growth and reproduction. End-of-century water warming and acidification conditions resulted in simulated faster growth for young surfclams and more energy allocated to reproduction until the beginning of the 22nd century when a reduction in maximum shell length and energy allocated to reproduction was observed for the RCP 8.5 scenario.
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Affiliation(s)
- Émilien Pousse
- National Research Council Post-Doctoral Associate at NOAA NMFS, 212 Rogers Ave, Milford, CT, 06418, USA
| | - Daphne Munroe
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Ave, Port Norris, NJ, 08349, USA
| | - Deborah Hart
- NOAA/NMFS, 166 Water St, Woods Hole, MA, 02543, USA
| | | | - Louise P Cameron
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, McLean 216, MS #08, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Jennie E Rheuban
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, McLean 216, MS #08, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Zhaohui Aleck Wang
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, McLean 216, MS #08, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Gary H Wikfors
- NOAA Fisheries Service, Northeast Fisheries Science Center, 212 Rogers Ave, Milford, CT, 06460, USA
| | - Shannon L Meseck
- NOAA Fisheries Service, Northeast Fisheries Science Center, 212 Rogers Ave, Milford, CT, 06460, USA.
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Kooijman SALM, Lika K, Augustine S, Marn N. Multidimensional scaling for animal traits in the context of dynamic energy budget theory. CONSERVATION PHYSIOLOGY 2021; 9:coab086. [PMID: 36531935 PMCID: PMC8677455 DOI: 10.1093/conphys/coab086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 12/09/2021] [Indexed: 06/15/2023]
Abstract
The method of multidimensional scaling (MDS) has long existed, but could only recently be applied to animal traits in the context of dynamic energy budget (DEB) theory. The application became possible because of the following: (i) the Add-my-Pet (AmP) collection of DEB parameters and traits (approximately 280) recently reached 3000 animal species with 45000 data sets of measurements; (ii) we found a natural distance measure for species based on their traits as a side result of our research on parameter estimation in DEB context; and (iii) we developed plotting code for visualization that allows labelling of taxonomic relationships. Traits, here defined as DEB parameters or any function of these parameters, have different dimensions, which hamper application of many popular distance measures since they (implicitly) assume that all traits have the same dimensions. The AmP collection follows the workflow that measured data determine parameters and parameters determine trait values. In this way we could fill up the species traits table completely, which we could not do by using measured values only, as data availability varies considerably between species and is typically poor. The goodness of fit of predictions for all data sets is generally excellent. This paper discusses links between the MDS method and parameter estimation and illustrates the application of MDS for the AmP collection to five taxa, three ectothermic and two endothermic, which we consider to be 'complete', in the sense that we expect that it will be difficult to find more species with data in the open literature. This application of MDS shows links between traits and taxonomy that supplements our efforts to find patterns in the co-variation of parameter values. Knowledge about metabolic performance is key to conservation biology, sustainable management and environmental risk assessment, which are seen as interlinked fields.
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Affiliation(s)
- Sebastiaan A L M Kooijman
- Department of Theoretical Biology, VU University Amsterdam, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Konstadia Lika
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Starrlight Augustine
- Akvaplan-niva AS, Fram High North Research Centre for Climate and the Environment, 9296 Tromsø, Norway
| | - Nina Marn
- Division for Environmental and Marine Research, Rudjer Bošković Institute, 10000 Zagreb, Croatia
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