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Chisholm RA, Kristensen NP, Rheindt FE, Chong KY, Ascher JS, Lim KKP, Ng PKL, Yeo DCJ, Meier R, Tan HH, Giam X, Yeoh YS, Seah WW, Berman LM, Tan HZ, Sadanandan KR, Theng M, Jusoh WFA, Jain A, Huertas B, Tan DJX, Ng ACR, Teo A, Yiwen Z, Cho TJY, Sin YCK. Two centuries of biodiversity discovery and loss in Singapore. Proc Natl Acad Sci U S A 2023; 120:e2309034120. [PMID: 38079550 PMCID: PMC10743369 DOI: 10.1073/pnas.2309034120] [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: 05/30/2023] [Accepted: 10/22/2023] [Indexed: 12/18/2023] Open
Abstract
There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for "dark extinctions," i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as-usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable.
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Affiliation(s)
- Ryan A. Chisholm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Nadiah P. Kristensen
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Kwek Yan Chong
- Singapore Botanic Gardens, National Parks Board, Singapore259569, Singapore
| | - John S. Ascher
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Kelvin K. P. Lim
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore117377, Singapore
| | - Peter K. L. Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore117377, Singapore
| | - Darren C. J. Yeo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore117377, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin10115, Germany
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore117377, Singapore
| | - Xingli Giam
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN37996
| | - Yi Shuen Yeoh
- Singapore Botanic Gardens, National Parks Board, Singapore259569, Singapore
| | - Wei Wei Seah
- Singapore Botanic Gardens, National Parks Board, Singapore259569, Singapore
| | - Laura M. Berman
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Hui Zhen Tan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Keren R. Sadanandan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
| | - Meryl Theng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA5005, Australia
| | - Wan F. A. Jusoh
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- School of Science, Monash University Malaysia, Subang Jaya47500, Malaysia
| | - Anuj Jain
- Nature Society (Singapore), Singapore389466, Singapore
- bioSEA Pte Ltd., Singapore679521, Singapore
| | - Blanca Huertas
- Department of Life Sciences, Natural History Museum, LondonSW7 5BD, United Kingdom
| | - David J. X. Tan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131
| | - Alicia C. R. Ng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Aloysius Teo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Zeng Yiwen
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
- Centre for Nature-based Climate Solutions, Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117546, Singapore
| | - Tricia J. Y. Cho
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
| | - Y. C. Keita Sin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore117558, Singapore
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Digging in a 120 years-old lunch: What can we learn from collection specimens of extinct species? PLoS One 2022; 17:e0270032. [PMID: 35793291 PMCID: PMC9258829 DOI: 10.1371/journal.pone.0270032] [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: 07/22/2021] [Accepted: 06/02/2022] [Indexed: 12/03/2022] Open
Abstract
Studying collection specimens is often the only way to unravel information about recent extinctions. These can reveal knowledge on threats and life traits related to extinction, and contribute, by extrapolation, to the conservation of extant species. However, high-throughput sequencing methods have rarely been applied to extinct species to reveal information on their ecology. Insular species are especially prone to extinction. We studied the gut contents of three specimens of the extinct giant skink Chioninia coctei of the Cabo Verde Islands using microscopy and DNA-metabarcoding. The presence of Tachygonetria adult nematodes suggests plants as important diet items. Our metabarcoding approach also identified plants and, additionally, invertebrates, supporting the hypothesis of C. coctei’s generalist diet. The absence of vertebrates in the digestive contents may reflect the decline of seabirds on the Desertas Islands that could have contributed to the debilitation of the giant skink, already depleted by persecution and severe droughts. Even with a small sample size, this study contributes to shedding light on the trophic roles of this enigmatic extinct species and emphasizes the need to develop holistic conservation plans for island threatened taxa. Additionally, it illustrates the potential of integrating up-to-date molecular methods with traditional approaches to studying collection specimens to help to solve ecological puzzles in other ecosystems.
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Abstract
The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the 'pre-taxonomic' period (approx. 1500-1800 CE) and, to some extent, in the 'taxonomic period' (approx. 1800-present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the 'taxonomic period'. For the 'pre-taxonomic period', simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the 'taxonomic period' (1800-present) and approximately 180 in the 'pre-taxonomic period' (1500-1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).
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Affiliation(s)
- Mannfred M A Boehm
- Department of Botany, Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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