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Feng X, Peterson AT, Aguirre-López LJ, Burger JR, Chen X, Papeş M. Rethinking ecological niches and geographic distributions in face of pervasive human influence in the Anthropocene. Biol Rev Camb Philos Soc 2024; 99:1481-1503. [PMID: 38597328 DOI: 10.1111/brv.13077] [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: 01/20/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Species are distributed in predictable ways in geographic spaces. The three principal factors that determine geographic distributions of species are biotic interactions (B), abiotic conditions (A), and dispersal ability or mobility (M). A species is expected to be present in areas that are accessible to it and that contain suitable sets of abiotic and biotic conditions for it to persist. A species' probability of presence can be quantified as a combination of responses to B, A, and M via ecological niche modeling (ENM; also frequently referred to as species distribution modeling or SDM). This analytical approach has been used broadly in ecology and biogeography, as well as in conservation planning and decision-making, but commonly in the context of 'natural' settings. However, it is increasingly recognized that human impacts, including changes in climate, land cover, and ecosystem function, greatly influence species' geographic ranges. In this light, historical distinctions between natural and anthropogenic factors have become blurred, and a coupled human-natural landscape is recognized as the new norm. Therefore, B, A, and M (BAM) factors need to be reconsidered to understand and quantify species' distributions in a world with a pervasive signature of human impacts. Here, we present a framework, termed human-influenced BAM (Hi-BAM, for distributional ecology that (i) conceptualizes human impacts in the form of six drivers, and (ii) synthesizes previous studies to show how each driver modifies the natural BAM and species' distributions. Given the importance and prevalence of human impacts on species distributions globally, we also discuss implications of this framework for ENM/SDM methods, and explore strategies by which to incorporate increasing human impacts in the methodology. Human impacts are redefining biogeographic patterns; as such, future studies should incorporate signals of human impacts integrally in modeling and forecasting species' distributions.
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Affiliation(s)
- Xiao Feng
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | - Joseph R Burger
- Department of Biology, University of Kentucky, Lexington, KY, 40502, USA
| | - Xin Chen
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Monica Papeş
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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2
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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-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: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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3
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Seal S, Bayyana S, Pande A, Ghanekar C, Hatkar PS, Pathan S, Patel S, Rajpurkar S, Prajapati S, Gole S, Iyer S, Nair A, Prabakaran N, Sivakumar K, Johnson JA. Spatial prioritization of dugong habitats in India can contribute towards achieving the 30 × 30 global biodiversity target. Sci Rep 2024; 14:13984. [PMID: 38886526 PMCID: PMC11183059 DOI: 10.1038/s41598-024-64760-8] [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: 10/18/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Indian coastal waters are critical for dugong populations in the western Indian Ocean. Systematic spatial planning of dugong habitats can help to achieve biodiversity conservation and area-based protection targets in the region. In this study, we employed environmental niche modelling to predict suitable dugong habitats and identify influencing factors along its entire distribution range in Indian waters. We examined data on fishing pressures collected through systematic interview surveys, citizen-science data, and field surveys to demarcate dugong habitats with varying risks. Seagrass presence was the primary factor in determining dugong habitat suitability across the study sites. Other variables such as depth, bathymetric slope, and Euclidean distance from the shore were significant factors, particularly in predicting seasonal suitability. Predicted suitable habitats showed a remarkable shift from pre-monsoon in Palk Bay to post-monsoon in the Gulf of Mannar, indicating the potential of seasonal dugong movement. The entire coastline along the Palk Bay-Gulf of Mannar region was observed to be at high to moderate risk, including the Gulf of Mannar Marine National Park, a high-risk area. The Andaman Islands exhibited high suitability during pre- and post-monsoon season, whereas the Nicobar Islands were highly suitable for monsoon season. Risk assessment of modelled suitable areas revealed that < 15% of high-risk areas across Andaman and Nicobar Islands and Palk Bay and Gulf of Mannar, Tamil Nadu, fall within the existing protected areas. A few offshore reef islands are identified under high-risk zones in the Gulf of Kutch, Gujarat. We highlight the utility of citizen science and secondary data in performing large-scale spatial ecological analysis. Overall, identifying synoptic scale 'Critical Dugong Habitats' has positive implications for the country's progress towards achieving the global 30 × 30 target through systematic conservation planning.
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Affiliation(s)
- Sohom Seal
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Sharad Bayyana
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
- Centre for Biodiversity and Conservation Science, School of Environment, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Anant Pande
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
- Marine Program, Wildlife Conservation Society - India, Bengaluru, Karnataka, 560 097, India
| | - Chinmaya Ghanekar
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Prachi Sachchidanand Hatkar
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Sameeha Pathan
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Shivani Patel
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Sagar Rajpurkar
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Sumit Prajapati
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Swapnali Gole
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Sweta Iyer
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Aditi Nair
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Nehru Prabakaran
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
| | - Kuppusamy Sivakumar
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India
- Department of Ecology and Environment, Pondicherry University, Puducherry, India
| | - Jeyaraj Antony Johnson
- Department of Habitat Ecology, Wildlife Institute of India, P.O. Chandrabani, Dehradun, Uttarakhand, 248 001, India.
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Ozawa H, Yoshihama T, Gishitomi S, Watanabe N, Ichikawa K, Sato K, Watanabe K, Takano K, Ochiai Y, Yamanaka H, Maruyama A. Fecal DNA analysis coupled with the sighting records re-expanded a known distribution of dugongs in Ryukyu Islands after half a century. Sci Rep 2024; 14:7957. [PMID: 38575626 PMCID: PMC10995173 DOI: 10.1038/s41598-024-58674-8] [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: 09/08/2023] [Accepted: 04/02/2024] [Indexed: 04/06/2024] Open
Abstract
DNA analysis of large herbivore feces samples collected from seagrass beds at two distant sites (Irabu Island in Miyako Islands and Kushi in Okinawa Island) in the Ryukyu Islands proved that some of these feces were from dugongs, which had been treated in recent studies as extinct in this region since the last stranding of a deceased individual in 2019. In addition, local knowledge of sightings of animals thought to be dugongs and confirmed cases of dugong feeding trails since 2010 were compiled to estimate its recent distribution. This is the first scientific report on the presence of this mammal in the Ryukyu Islands within the last four years, and particularly in the Miyako Islands within the last half-century. As the Ryukyu Islands are known to be the northern limit of the dugong's fragmented distribution in East Asia, conservation efforts are therefore needed.
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Affiliation(s)
- Hiroyuki Ozawa
- Incorporated Foundation Okinawa Prefecture Environment Science Center, Urasoe, Okinawa, 901-2111, Japan.
| | | | - Shogo Gishitomi
- Incorporated Foundation Okinawa Prefecture Environment Science Center, Urasoe, Okinawa, 901-2111, Japan
| | - Natsuki Watanabe
- Incorporated Foundation Okinawa Prefecture Environment Science Center, Urasoe, Okinawa, 901-2111, Japan
| | - Kotaro Ichikawa
- Field Science Education and Research Center, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Keiichi Sato
- Okinawa Churashima Foundation, Kunigami, Okinawa, 905-0206, Japan
| | - Kenta Watanabe
- National Institute of Technology, Okinawa College, Nago, Okinawa, 905-2192, Japan
| | | | - Yosuke Ochiai
- Japan Broadcasting Corporation, Shibuya, Tokyo, 150-8001, Japan
| | - Hiroki Yamanaka
- Center for Biodiversity Science, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi Maruyama
- Faculty of Advanced Science and Technology, Ryukoku University, Otsu, Shiga, 520-2194, Japan
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Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
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Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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6
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Lin M, Turvey ST, Liu M, Ma H, Li S. Lessons from extinctions of dugong populations. Science 2022; 378:148. [PMID: 36227965 DOI: 10.1126/science.ade9750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Mingming Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Heidi Ma
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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