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Ren X, Ma X, Allen E, Fang Y, Wen S. DNA Barcoding Technology Used to Successfully Sub-Classify a Museum Whale Specimen as Balaenoptera edeni edeni. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.921106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding technology is becoming an increasingly powerful tool in resolving issues of detailed species identification based on morphology, as commonly employed by museums. In the present study, we aimed to identify a stranded Bryde’s whale on Hainan Island, China by extracting DNA from a vertebra pre-treated by physical and/or chemical processes. Based on morphological characteristics, this Bryde’s whale was initially determined as Balaenoptera edeni. Then, DNA was efficiently extracted using ancient DNA techniques. The mitochondrial gene (COI) phylogenetic analysis further revealed that this museum whale specimen belonged to the sub-species B. e. edeni. This study provides a testable and rapid method for museum species verification, by using ancient DNA extraction methods to compensate the disadvantage of traditional DNA extraction methods that are difficult to extract valid DNA.
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Segre PS, di Clemente J, Kahane‐Rapport SR, Gough WT, Meÿer MA, Lombard AT, Goldbogen JA, Penry GS. High‐speed chases along the seafloor put Bryde's whales at risk of entanglement. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Paolo S. Segre
- Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Jacopo di Clemente
- Department of Biology University of Copenhagen Copenhagen Denmark
- Department of Biology University of Southern Denmark Odense Denmark
- Department of Ecoscience Aarhus University Aarhus Denmark
| | - Shirel R. Kahane‐Rapport
- Hopkins Marine Station of Stanford University Pacific Grove California USA
- Department of Biological Science California State University Fullerton California USA
| | - William T. Gough
- Hopkins Marine Station of Stanford University Pacific Grove California USA
| | - Michael A. Meÿer
- Department of Forestry, Fisheries and Environment, Branch: Oceans and Coasts Cape Town South Africa
- South African Whale Disentanglement Network (SAWDN) Cape Town South Africa
| | - Amanda T. Lombard
- Institute for Coastal and Marine Research, Nelson Mandela University Gqeberha South Africa
| | | | - Gwenith S. Penry
- Institute for Coastal and Marine Research, Nelson Mandela University Gqeberha South Africa
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Ghosh PN, Verster R, Sewell TR, O'Hanlon SJ, Brookes LM, Rieux A, Garner TWJ, Weldon C, Fisher MC. Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR. Mol Ecol Resour 2021; 21:1452-1459. [PMID: 33232563 PMCID: PMC8651002 DOI: 10.1111/1755-0998.13299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 11/28/2022]
Abstract
The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage‐specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates. see also the Perspective by Claudio Azat
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Affiliation(s)
- Pria N Ghosh
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.,Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Thomas R Sewell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Simon J O'Hanlon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lola M Brookes
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.,Institute of Zoology, Zoological Society of London, London, UK.,The Royal Veterinary College, Hatfield, UK
| | - Adrien Rieux
- CIRAD, UMR, PVBMT, St Pierre, La Réunion, France
| | - Trenton W J Garner
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.,Institute of Zoology, Zoological Society of London, London, UK
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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Purdon J, Shabangu FW, Yemane D, Pienaar M, Somers MJ, Findlay K. Species distribution modelling of Bryde's whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies. PeerJ 2020; 8:e9997. [PMID: 33024637 PMCID: PMC7518163 DOI: 10.7717/peerj.9997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/28/2020] [Indexed: 11/20/2022] Open
Abstract
In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde's whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde's whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas.
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Affiliation(s)
- Jean Purdon
- Whale Unit, Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Fannie W Shabangu
- Fisheries Management Branch, Department of Environment, Forestry and Fisheries, Cape Town, South Africa
| | - Dawit Yemane
- Fisheries Management Branch, Department of Environment, Forestry and Fisheries, Cape Town, South Africa.,University of Cape Town, Marine Research Institute, Cape Town, Western Cape, South Africa
| | - Marc Pienaar
- uLwazi Node, South African Environmental Observation Network, Pretoria, South Africa
| | - Michael J Somers
- Mammal Research Institute, Centre for Invasion Biology, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ken Findlay
- Centre for Sustainable Oceans, Cape Peninsula University of Technology, Cape Town, South Africa
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A hidden Markov model with selective time domain feature extraction to detect inshore Bryde's whale short pulse calls. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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