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Gruppi C, Sanzenbacher P, Balekjian K, Hagar R, Hagen S, Rayne C, Schweizer TM, Bossu CM, Cooper D, Dietsch T, Smith TB, Ruegg K, Harrigan RJ. Genetic identification of avian samples recovered from solar energy installations. PLoS One 2023; 18:e0289949. [PMID: 37672506 PMCID: PMC10482291 DOI: 10.1371/journal.pone.0289949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/30/2023] [Indexed: 09/08/2023] Open
Abstract
Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots"-known to be of avian origin but not readily assignable to species via morphology-may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.
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Affiliation(s)
- Cristian Gruppi
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Peter Sanzenbacher
- U.S. Fish and Wildlife Service, Palm Springs, California, United States of America
| | - Karina Balekjian
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rachel Hagar
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Sierra Hagen
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Christine Rayne
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Teia M. Schweizer
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Christen M. Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Daniel Cooper
- Resource Conservation District, Santa Monica Mountains, Topanga, California, United States of America
| | - Thomas Dietsch
- U.S. Fish and Wildlife Service, Carlsbad, California, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
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Chen W, Miao K, Liu Y, Zhang J, Zhao Y, Hu D, Wang P, Li P, Chang Q, Hu C. Using DNA barcoding and field surveys to guide wildlife management at Nanjing Lukou International Airport, China. Ecol Evol 2023; 13:e10005. [PMID: 37066064 PMCID: PMC10099200 DOI: 10.1002/ece3.10005] [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: 02/09/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023] Open
Abstract
The conflicts between wildlife and aircraft have increased due to the development of the aviation industry. While many studies have quantified the relative hazards of wildlife to aircraft, few studies have combined DNA barcoding techniques with field surveys of bird communities in different habitats to reveal the exact species involved in bird strikes and how the habitat heterogeneity around airports affects bird communities and even the occurrence of bird strikes. Taking Nanjing Lukou International Airport in China as an example, based on the DNA barcoding technology and detailed field research, we establish the most commonly struck species, which can help managers identify the level of hazard and lead to meaningful reductions in hazards and costs associated with bird strike. The investigation of bird communities showed that there were 149 bird species recorded within an 8 km radius. There were 89, 88, 61, and 88 species in the woodland, wetland, farmland, and urban area, respectively. In total, 303 samples identified 82 species representing 13 orders and 32 family of birds from bird strike cases, of which 24 species were not found in the field survey. Passeriformes were the most common order of birds identified, with 43 species represented in 167 identifications. Skylark, Thrush, Shrike, Lapwing, and Swallow were most likely to cause damage or substantial damage to aircraft when strikes occurred. In addition to birds, we identified 69 bats individuals (accounting for 22.77%) using DNA barcoding. The Bray-Curtis similarity analysis revealed that species involved in bird strike had the highest similarity with urban area. Our findings suggest that policymakers should pay more attention to managing the wetlands and urban areas surrounding the airport. These findings imply that DNA barcoding can add to the environmental monitoring in airports, which can facilitate hazard management and improve air safety.
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Affiliation(s)
- Wan Chen
- College of Environment and EcologyJiangsu Open University (The City Vocational College of Jiangsu)NanjingJiangsuChina
| | - Keer Miao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
| | - Yizheng Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
| | - Jie Zhang
- China Academy of Civil Aviation Science and TechnologyBeijingChina
| | - Yang Zhao
- Nanjing Lukou International AirportNanjingJiangsuChina
| | - Dongfang Hu
- Nanjing Lukou International AirportNanjingJiangsuChina
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life SciencesNanjing Normal UniversityNanjingJiangsuChina
- Analytical and Testing CenterNanjing Normal UniversityNanjingJiangsuChina
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Tizard J, Patel S, Waugh J, Tavares E, Bergmann T, Gill B, Norman J, Christidis L, Scofield P, Haddrath O, Baker A, Lambert D, Millar C. DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation. BMC Evol Biol 2019; 19:52. [PMID: 30744573 PMCID: PMC6369544 DOI: 10.1186/s12862-019-1346-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/02/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. RESULTS We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. CONCLUSIONS DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.
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Affiliation(s)
- Jacqueline Tizard
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - John Waugh
- Unitec Institute of Technology, Auckland, New Zealand
| | - Erika Tavares
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
- Present address: Laboratory Research Project Manager, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tjard Bergmann
- Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17d, D-30559, Hannover, Germany
| | - Brian Gill
- Associate Emeritus, Auckland War Memorial Museum, Private Bag 92018, Auckland, 1142, New Zealand
| | - Janette Norman
- Molecular Biology Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
- Present address: Graduate School, Southern Cross University, Lismore, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Paul Scofield
- Canterbury Museum, Rolleston Ave, Christchurch, 8001, New Zealand
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - Allan Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Brisbane, Queensland, 4111, Australia
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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Coghlan ML, White NE, Murray DC, Houston J, Rutherford W, Bellgard MI, Haile J, Bunce M. Metabarcoding avian diets at airports: implications for birdstrike hazard management planning. INVESTIGATIVE GENETICS 2013; 4:27. [PMID: 24330620 PMCID: PMC3874626 DOI: 10.1186/2041-2223-4-27] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/14/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Wildlife collisions with aircraft cost the airline industry billions of dollars per annum and represent a public safety risk. Clearly, adapting aerodrome habitats to become less attractive to hazardous wildlife will reduce the incidence of collisions. Formulating effective habitat management strategies relies on accurate species identification of high-risk species. This can be successfully achieved for all strikes either through morphology and/or DNA-based identifications. Beyond species identification, dietary analysis of birdstrike gut contents can provide valuable intelligence for airport hazard management practices in regards to what food is attracting which species to aerodromes. Here, we present birdstrike identification and dietary data from Perth Airport, Western Australia, an aerodrome that saw approximately 140,000 aircraft movements in 2012. Next-generation high throughput DNA sequencing was employed to investigate 77 carcasses from 16 bird species collected over a 12-month period. Five DNA markers, which broadly characterize vertebrates, invertebrates and plants, were used to target three animal mitochondrial genes (12S rRNA, 16S rRNA, and COI) and a plastid gene (trnL) from DNA extracted from birdstrike carcass gastrointestinal tracts. RESULTS Over 151,000 DNA sequences were generated, filtered and analyzed by a fusion-tag amplicon sequencing approach. Across the 77 carcasses, the most commonly identified vertebrate was Mus musculus (house mouse). Acrididae (grasshoppers) was the most common invertebrate family identified, and Poaceae (grasses) the most commonly identified plant family. The DNA-based dietary data has the potential to provide some key insights into feeding ecologies within and around the aerodrome. CONCLUSIONS The data generated here, together with the methodological approach, will greatly assist in the development of hazard management plans and, in combination with existing observational studies, provide an improved way to monitor the effectiveness of mitigation strategies (for example, netting of water, grass type, insecticides and so on) at aerodromes. It is hoped that with the insights provided by dietary data, airports will be able to allocate financial resources to the areas that will achieve the best outcomes for birdstrike reduction.
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Affiliation(s)
- Megan L Coghlan
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
| | - Nicole E White
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
| | - Dáithí C Murray
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
| | - Jayne Houston
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
| | - William Rutherford
- Ornithological Technical Services, Welshpool, Western Australia 6106,
Australia
| | - Matthew I Bellgard
- Center for Comparative Genomics, Murdoch University, Murdoch, Western
Australia 6150, Australia
| | - James Haile
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
| | - Michael Bunce
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of
Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia
6150, Australia
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Joo S, Park S. Identification of bird species and their prey using DNA barcode on feces from Korean traditional village groves and forests (maeulsoop). Anim Cells Syst (Seoul) 2012. [DOI: 10.1080/19768354.2012.720939] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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DUPUIS JULIANR, ROE AMANDAD, SPERLING FELIXAH. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol 2012; 21:4422-36. [DOI: 10.1111/j.1365-294x.2012.05642.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Lijtmaer DA, Kerr KCR, Stoeckle MY, Tubaro PL. DNA barcoding birds: from field collection to data analysis. Methods Mol Biol 2012; 858:127-152. [PMID: 22684955 DOI: 10.1007/978-1-61779-591-6_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5' end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens.
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Federhen S. Comment on 'Birdstrikes and barcoding: can DNA methods help make the airways safer?'. Mol Ecol Resour 2011; 11:937-8; discussion 939-42. [PMID: 21899722 PMCID: PMC3224856 DOI: 10.1111/j.1755-0998.2011.03054.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
GenBank is the database of record for public sequence data. Results reported in the scientific literature that are based on sequence data cannot be evaluated if the underlying data is not in the public record.
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Affiliation(s)
- Scott Federhen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Bethesda, MD 20894, USA.
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Corrigendum. Mol Ecol Resour 2011. [DOI: 10.1111/j.1755-0998.2011.03062.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Affiliation(s)
- S. RATNASINGHAM
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - P. D. N. HEBERT
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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MILLAR CRAIGD, WAUGH JOHN, LAMBERT DAVIDM. Are BOLD searches scientific? A response to Federhen (2011). Mol Ecol Resour 2011. [DOI: 10.1111/j.1755-0998.2011.03066.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- CRAIG D. MILLAR
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - JOHN WAUGH
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Natural Sciences, Massey University, Private Bag 102 904, NSMC, Auckland, New Zealand
| | - DAVID M. LAMBERT
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Qld 4111, Australia
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Lijtmaer DA, Kerr KCR, Barreira AS, Hebert PDN, Tubaro PL. DNA barcode libraries provide insight into continental patterns of avian diversification. PLoS One 2011; 6:e20744. [PMID: 21818252 PMCID: PMC3144888 DOI: 10.1371/journal.pone.0020744] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 05/11/2011] [Indexed: 12/01/2022] Open
Abstract
Background The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries. Methodology and Principal Findings Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity. Conclusions and Significance DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.
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Affiliation(s)
- Darío A Lijtmaer
- División Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Buenos Aires, Argentina.
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