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Jaito W, Sonongbua J, Panthum T, Wattanadilokcahtkun P, Ariyaraphong N, Thong T, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Han K, Antunes A, Sitdhibutr R, Koga A, Duengkae P, Kasorndorkbua C, Srikulnath K. Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories. Genes Genomics 2024; 46:95-112. [PMID: 37985545 DOI: 10.1007/s13258-023-01462-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: 08/17/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data. OBJECTIVE Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae). METHODS Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed. RESULTS The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively. CONCLUSION Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Jumaporn Sonongbua
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Kom Ko, Mueang Nong Khai District, Nong Khai, 43000, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokcahtkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Ratiwan Sitdhibutr
- Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Chaiyan Kasorndorkbua
- Raptor Rehabilitation Unit, Kasetsart University Veterinary Teaching Hospital Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand.
- Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand.
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
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Kim JI, Do TD, Yeo Y, Kim CB. Comparative analysis of complete mitochondrial genomes of three Trichoglossus species (Psittaciformes: Psittacidae). Mol Biol Rep 2022; 49:9121-9127. [PMID: 35941414 DOI: 10.1007/s11033-022-07791-6] [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: 04/01/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The genus Trichoglossus belongs to the family Psittacidae and includes fourteen species distributed worldwide. According to the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species, most Trichoglossus species have shown a decreasing population trend recently. In particular, Trichoglossus forsteni is listed as "Endangered" in the IUCN Red List of Threatened Species. Moreover, Trichoglossus haematodus and Trichoglossus moluccanus are one of the most traded and illegally traded parrots. However, only a few genetic studies have been conducted regarding the conservation of this genus. METHODS AND RESULTS In the present study, complete mitochondrial genomes of three species (T. forsteni, T. haematodus, and T. moluccanus) were sequenced and compared with Trichoglossus rubritorquis, species whose mitochondrial genome is already reported. Results indicate that the complete mitochondrial genomes of the three species were similar in length (17,906 bp for T. haematodus to 17,909 bp for T. forsteni). Furthermore, the organization and order of these three mitochondrial genomes were identical, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two control regions (CRs) categorized into three domains containing nine conserved motifs. In addition, the genus Trichoglossus formed a well-supported monophyletic lineage. CONCLUSIONS The results of this study may be useful for future genetic studies toward the conservation of the genus Trichoglossus.
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Affiliation(s)
- Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong, Vietnam
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea.
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Kim JI, Do TD, Choi Y, Yeo Y, Kim CB. Characterization and Comparative Analysis of Complete Mitogenomes of Three Cacatua Parrots (Psittaciformes: Cacatuidae). Genes (Basel) 2021; 12:genes12020209. [PMID: 33572592 PMCID: PMC7910981 DOI: 10.3390/genes12020209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cacatua alba, Cacatua galerita, and Cacatua goffiniana are parrots of the family Cacatuidae. Wild populations of these species are declining with C. alba listed by the International Union for the Conservation of Nature and Natural Resources (IUCN) as Endangered. In this study, complete mitogenomes were sequenced for a comparative analysis among the Cacatua species, and a detailed analysis of the control region. Mitogenome lengths of C. alba,C. galerita, and C. goffiniana were 18,894, 18,900, and 19,084 bp, respectively. They included 13 protein coding genes, two ribosomal RNA genes, 24 transfer RNA genes, three degenerated genes, and two control regions. Ten conserved motifs were found in three domains within each of the two control regions. For an evolution of duplicated control regions of Cacatua, domain I and the 3′ end of domain III experienced an independent evolution, while domain II and most of the regions of domain III was subjected to a concerted evolution. Based on a phylogenetic analysis of 37 mitochondrial genes, the genus Cacatua formed a well-supported, monophyletic, crown group within the Cacatuidae. Molecular dating results showed that Cacatua diverged from other genera of Cacatuinae in the middle of Miocene.
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Affiliation(s)
- Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yisoo Choi
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon 13829, Korea;
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
- Correspondence: ; Tel.: +82-2-2287-5288
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West RG, Mathias DK, Day JF, Acevedo C, Unnasch TR, Burkett-Cadena ND. Seasonal Changes of Host Use by Culiseta melanura (Diptera: Culicidae) in Central Florida. JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1627-1634. [PMID: 32280994 DOI: 10.1093/jme/tjaa067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Indexed: 06/11/2023]
Abstract
The mosquito Culiseta melanura (Coquillett) is the primary enzootic vector of eastern equine encephalitis virus (EEEV), a zoonotic Alphavirus endemic to eastern North America. In its northern range, Cs. melanura is considered a strict avian biter, transmitting EEEV among susceptible birds in a cycle of enzootic amplification. In its southern range, however, Cs. melanura is more general in host use, feeding heavily upon birds but also reptiles and mammals. The goal of this study was to better understand how host use of Cs. melanura changes throughout the year in Florida, where year-round EEEV transmission is observed. Mosquitoes were sampled in 2018 from nine sites across three central Florida counties. In total, 213 Cs. melanura bloodmeals were identified by PCR consisting of 39 species of birds, reptiles, and mammals. Avian bloodmeals were prominent throughout the year (range = 30-85%), and songbirds were a large portion of identified bloodmeals (37.1%). Reptiles surpassed birds only in spring (April-June), and brown anole (Anolis sagrei Duméril and Bibron, 1837 [Reptilia: Dactyloidae]) was the most commonly detected single host species (22.1% overall). Mammalian bloodmeals were mainly observed in summer, with humans being the most fed on mammal (12.7% overall). This study reveals that in southern foci of EEEV transmission, Cs. melanura host use varies throughout the year with reptiles providing the majority of blood meals in spring (51.3%), and birds are fed on more than other host groups during all other seasons (50.6-70.1%). In addition, feeding on mammals increases during summer months, which may implicate Cs. melanura in epizootic transmission in Florida.
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Affiliation(s)
- Richard G West
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th Street SE, Vero Beach, FL
| | - Derrick K Mathias
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th Street SE, Vero Beach, FL
| | - Jonathan F Day
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th Street SE, Vero Beach, FL
| | - Carolina Acevedo
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th Street SE, Vero Beach, FL
| | - Thomas R Unnasch
- Global Health Infectious Disease Research Program, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th Street SE, Vero Beach, FL
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Hoyer IJ, Acevedo C, Wiggins K, Alto BW, Burkett-Cadena ND. Patterns of Abundance, Host Use, and Everglades Virus Infection in Culex (Melanoconion) cedecei Mosquitoes, Florida, USA. Emerg Infect Dis 2019; 25:1093-1100. [PMID: 31107225 PMCID: PMC6537747 DOI: 10.3201/eid2506.180338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Everglades virus (EVEV), subtype II within the Venezuelan equine encephalitis (VEE) virus complex, is a mosquitoborne zoonotic pathogen endemic to south Florida, USA. EVEV infection in humans is considered rare, probably because of the sylvatic nature of the vector, the Culex (Melanoconion) cedecei mosquito. The introduction of Cx. panocossa, a tropical vector mosquito of VEE virus subtypes that inhabits urban areas, may increase human EVEV exposure. Field studies investigating spatial and temporal patterns of abundance, host use, and EVEV infection of Cx. cedecei mosquitoes in Everglades National Park found that vector abundance was dynamic across season and region. Rodents, particularly Sigmodon hispidus rats, were primary vertebrate hosts, constituting 77%–100% of Cx. cedecei blood meals. Humans were fed upon at several locations. We detected EVEV infection in Cx. cedecei mosquitoes in lower and upper regions of Everglades National Park only during the wet season, despite an abundance of Cx. cedecei mosquitoes at other sampling times.
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Dinh TD, Ngatia JN, Cui LY, Ma Y, Dhamer TD, Xu YC. Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Sci Int Genet 2019; 40:85-95. [PMID: 30780122 DOI: 10.1016/j.fsigen.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023]
Abstract
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.
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Affiliation(s)
- Thi Dao Dinh
- College of Wildlife Resources, Northeast Forestry University, China
| | | | - Liang Yu Cui
- College of Wildlife Resources, Northeast Forestry University, China
| | - Yue Ma
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China
| | | | - Yan Chun Xu
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China; State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, China.
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PREFLEDGING MORTALITY AND THE ABUNDANCE OF MOSQUITOES BITING NESTLING BARN OWLS ( TYTO ALBA) IN FLORIDA, USA. J Wildl Dis 2019; 55:597-607. [PMID: 30702952 DOI: 10.7589/2017-12-307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mosquito-borne diseases can have disastrous effects on avian populations; therefore, most studies of bird and mosquito interactions have focused on the mortality and morbidity associated with the diseases. However, the effect of mosquitoes feeding on birds, independent of disease, has not been well studied. We studied Barn Owls (Tyto alba) nesting in artificial nest boxes in sugarcane (Saccharum officinarum) fields in Florida, US. To reduce mosquito effects on nestlings, we used an insecticide spray in half of the nest boxes. Mosquito suction traps were fixed to the outside of eight nest boxes (four treated and four untreated) to collect mosquitoes over a 24-h period (one trap night) once weekly, from incubation until all nestlings fledged. Collected mosquitoes were counted, sorted into blood-fed and unfed females, and identified to species when possible. The dominant mosquito species captured were Culex nigripalpus, Mansonia dyari, and Mansonia titillans. The highest total number of mosquitoes and blood-fed mosquitoes captured in a suction trap in one trap night was 3,193 and 379, respectively. Overall, significantly fewer mosquitoes were captured from treated nest boxes compared to untreated boxes. Nestling age influenced the total number of mosquitoes captured, with the highest numbers associated with fledglings 22-42 d old. The highest numbers of blood-fed mosquitoes were captured when nestlings were 22-28 d old. Nestlings in insecticide-treated boxes had higher survival rates compared to those in untreated boxes during months with high mosquito numbers. Mosquitoes can impose energetic costs on nestlings by causing stress from irritation, dehydration, and the constant regeneration of blood cells. These costs, in addition to factors such as food shortage, temperature, and overall health of the nestling, can contribute to higher mortality rates during nesting periods with high mosquito numbers.
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Stenn T, Peck KJ, Rocha Pereira G, Burkett-Cadena ND. Vertebrate Hosts of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus (Diptera: Culicidae) as Potential Vectors of Zika Virus in Florida. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:10-17. [PMID: 30165498 DOI: 10.1093/jme/tjy148] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Zika virus (ZIKV), once considered an obscure pathogen, spread rapidly from 2014 to 2016 to become an internationally notifiable condition of major public health concern. The relative importance of various Culex and Aedes species mosquitoes (Diptera: Culicidae) in ZIKV transmission is a topic of debate. Quantifying host use is important in determining the vectorial capacity of a mosquito species for transmitting ZIKV in nature. In the United States, few data are available on host use of Aedes aegypti L. (Diptera: Culicidae) and Aedes albopictus (Skuse) (Diptera: Culicidae), confirmed and suspected vectors of ZIKV, respectively. Here, we report results of bloodmeal analysis to quantify host use of confirmed (Ae. aegypti) and suspected (Ae. albopictus and Culex quinquefasciatus Say (Diptera: Culicidae)) vectors of ZIKV in two Florida counties. At an auto salvage yard in Indian River County, Ae. aegypti, Ae. albopictus and Cx. quinquefasciatus fed mainly on humans, taking 90.2, 90.8, and 78.6% of bloodmeals from humans, respectively. At a residential area in Martin County, Ae. aegypti, Ae. albopictus took 61.5 and 66.7% of bloodmeals from humans, higher than Cx. quinquefasciatus (11.1%). Patterns of host use suggest that Ae. aegypti and Ae. albopictus are the most likely vectors of ZIKV in Florida and that Cx. quinquefasciatus would likely play a lesser role in ZIKV transmission in Florida. However, the relative importance of the three species in ZIKV transmission is likely location and population specific. Detailed studies quantifying other parameters of vectorial capacity, including vector competence, are needed in order to determine the actual role for each species in ZIKV transmission.
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Affiliation(s)
- Tanise Stenn
- Florida Medical Entomology Laboratory, University of Florida IFAS, Vero Beach, FL
| | - Karlette J Peck
- Florida Department of Health Martin-County, SE Willoughby Boulevard, Stuart, FL
| | - Glauber Rocha Pereira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil, Manguinhos, Rio de Janeiro, Brasil
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Summerell AE, Frankham GJ, Gunn P, Johnson RN. DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade. Forensic Sci Int 2018; 295:46-53. [PMID: 30554021 DOI: 10.1016/j.forsciint.2018.11.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022]
Abstract
The illegal trade in wild animals being sold as 'captive bred' is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. As this species is distributed throughout Australia and in New Guinea (currently comprising of five recognised sub-species), this project aimed to develop a DNA based method to definitively determine the source country of an echidna and explore the use of non-invasive sampling techniques. Here we use non-invasively sampled echidna quills and demonstrate the extraction of mitochondrial DNA and amplification of a region of the mitochondrial genome. Phylogenetically informative markers for analysis of a 322bp segment of the D-loop region were developed, and subsequently validated, using animals with known source locations allowing us to reliably distinguish between echidnas from New Guinea, and Australia. This research presents the first validated forensic protocols for short beaked echidnas and will be an integral tool in understanding the movement of animals in this emerging trade.
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Affiliation(s)
- A E Summerell
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, Australia; Centre for Forensic Science, University of Technology Sydney, 15 Broadway, Ultimo, Australia.
| | - G J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, Australia
| | - P Gunn
- Centre for Forensic Science, University of Technology Sydney, 15 Broadway, Ultimo, Australia
| | - R N Johnson
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, Australia.
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Blosser EM, Lord CC, Stenn T, Acevedo C, Hassan HK, Reeves LE, Unnasch TR, Burkett-Cadena ND. Environmental Drivers of Seasonal Patterns of Host Utilization by Culiseta melanura (Diptera: Culicidae) in Florida. JOURNAL OF MEDICAL ENTOMOLOGY 2017; 54:1365-1374. [PMID: 28874017 PMCID: PMC5850491 DOI: 10.1093/jme/tjx140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 06/07/2023]
Abstract
Field studies were carried out in four Florida counties to investigate winter and spring ecology of host use by Culiseta melanura (Coquillet), the primary vector of eastern equine encephalomyelitis virus (EEEV) in North America. Bloodmeal analysis by PCR was used to identify 233 host bloodmeals, which mainly originated from birds (78.5%) and reptiles (17.2%), primarily Anolis spp. lizards. Across counties, the percentage of bloodmeals from reptiles (7-37% depending upon county) increased with increasing day length and temperature in the spring. Multiple logistic regression revealed that differences in reptile host use across collection sites were largely explained by differences in average day length and temperature on the day of collection, and is probably owing to environment-driven behavioral patterns of ectothermic animals. Although past studies have demonstrated reptile biting by epizootic vectors of EEEV, including Culex (Melanoconion) spp., this is the first study to demonstrate widespread and common feeding upon ectothermic hosts by Cs. melanura. This work suggests that reptiles, particularly anole lizards, play a role in the ecology of EEEV in Florida either as amplifying hosts or as noncompetent hosts which dilute vector feedings thereby suppressing transmission. Detailed laboratory studies investigating impacts of environmental variables (temperature and photoperiod) on EEEV competence of anoles are needed to assess whether these animals support virus amplification.
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Affiliation(s)
- Erik M. Blosser
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th St. SE, Vero Beach, FL 32962 (; ; ; ; )
| | - Cynthia C. Lord
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th St. SE, Vero Beach, FL 32962 (; ; ; ; )
| | - Tanise Stenn
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th St. SE, Vero Beach, FL 32962 (; ; ; ; )
| | - Carolina Acevedo
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th St. SE, Vero Beach, FL 32962 (; ; ; ; )
| | - Hassan K. Hassan
- Department of Global Health, College of Public Health, Global Health Infectious Disease Research Program, University of South Florida, 3720 Spectrum Blvd., Suite 304, Tampa, FL 33612 (; )
| | - Lawrence E. Reeves
- Entomology and Nematology Department, University of Florida, PO Box 110620, Gainesville, FL 32611 ()
| | - Thomas R. Unnasch
- Department of Global Health, College of Public Health, Global Health Infectious Disease Research Program, University of South Florida, 3720 Spectrum Blvd., Suite 304, Tampa, FL 33612 (; )
| | - Nathan D. Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida IFAS, 200 9th St. SE, Vero Beach, FL 32962 (; ; ; ; )
- Corresponding author, e-mail:
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Blosser EM, Stenn T, Acevedo C, Burkett-Cadena ND. Host use and seasonality of Culex (Melanoconion) iolambdis (Diptera: Culicidae) from eastern Florida, USA. Acta Trop 2016; 164:352-359. [PMID: 27712940 DOI: 10.1016/j.actatropica.2016.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/28/2016] [Accepted: 10/02/2016] [Indexed: 01/17/2023]
Abstract
Culex (Melanoconion) iolambdis (Dyar, 1918) is a mosquito (Diptera: Culicidae) species found throughout much of tropical America, including southern Florida. Relatively few reports are available regarding the ecology of Cx. iolambdis, despite its widespread distribution and putative involvement in transmission of Venezuelan equine encephalitis virus. To quantify habitat and host utilization, adults of Cx. iolambdis were sampled from resting shelters at a field site in Vero Beach, Florida, over a 12-month period. Culex iolambdis (1109 males, 3072 females) constituted more than half (56.76%) of all mosquitoes sampled (24 species) and was active year-round. Unfed females and gravid females of Cx. iolambdis were significantly more abundant in mangrove habitat, while males and blood-fed females were not. PCR-based bloodmeal analysis of 305 females revealed that Cx. iolambdis has very wide host breadth, feeding on birds (37.0% overall), reptiles (26.6%), amphibians (23.3%) and mammals (13.1%). Green heron (Butorides virescens), Southern leopard frog (Lithobates sphenocephala) and American alligator (Alligator mississippiensis) were the most commonly fed upon hosts. Bloodmeals from different host classes varied significantly with season, suggesting that Cx. iolambdis may play a role in the amplification and epidemic transmission of zoonotic arboviruses affecting human health.
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Affiliation(s)
- Erik M Blosser
- Florida Medical Entomology Laboratory, Entomology and Nematology Department, University of Florida, 200 9(th) St. SE, Vero Beach, FL 32962, USA
| | - Tanise Stenn
- Florida Medical Entomology Laboratory, Entomology and Nematology Department, University of Florida, 200 9(th) St. SE, Vero Beach, FL 32962, USA
| | - Carolina Acevedo
- Florida Medical Entomology Laboratory, Entomology and Nematology Department, University of Florida, 200 9(th) St. SE, Vero Beach, FL 32962, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, Entomology and Nematology Department, University of Florida, 200 9(th) St. SE, Vero Beach, FL 32962, USA.
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Abstract
The illegal trade in ivory and rhino horn has led to a catastrophic decline in elephant and rhino populations worldwide. These iconic high profile species are one part of the illegal trade in wildlife products that threatens these species and the ecological balance in the habitats in which they live. Identification of the species present is required to determine that the trade is illegal and contrary to national legislation. This chapter details a robust DNA technique using part of the cytochrome b gene on the mitochondrial genome that will work on poor quality samples such as powdered horn or ivory products including statues and carvings. An appropriate DNA extraction technique is required to obtain at least 1 ng of DNA from which the amplification of part of the cytochrome b gene using universal primers is performed. This produces a fragment of 486 bp in size which can be sequenced using standard technologies. The resulting sequences are then aligned to voucher specimens or sequences on reliable databases. Analyses of the data should lead to confident species identification.
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Affiliation(s)
- Adrian Linacre
- Department of Biological Sciences, Flinders University, Box 2100, Adelaide, 5001, SA, Australia.
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan ROC
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13
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Wang LP, Geng RQ, Liu ZQ. An effective strategy for species identification of avian meats using the mitochondrial 12S rRNA gene fragment. ACTA ACUST UNITED AC 2014; 26:171-4. [DOI: 10.3109/19401736.2013.845769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Johnson RN, Wilson-Wilde L, Linacre A. Current and future directions of DNA in wildlife forensic science. Forensic Sci Int Genet 2013; 10:1-11. [PMID: 24680123 DOI: 10.1016/j.fsigen.2013.12.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022]
Abstract
Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Centre for Wildlife Genomics, Science and Learning Division, Australian Museum, Sydney, Australia.
| | - Linzi Wilson-Wilde
- Australia New Zealand Policing Advisory Agency - National Institute of Forensic Science, Melbourne, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, Australia
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Coghlan ML, White NE, Parkinson L, Haile J, Spencer PBS, Bunce M. Egg forensics: an appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Sci Int Genet 2011; 6:268-73. [PMID: 21741338 PMCID: PMC7102845 DOI: 10.1016/j.fsigen.2011.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/12/2011] [Accepted: 06/13/2011] [Indexed: 10/29/2022]
Abstract
Psittaciformes (parrots and cockatoos) are charismatic birds, their plumage and capacity for learning make them highly sought after pets. The illegal trade in parrots and cockatoos poses a serious threat to the viability of native populations; in addition, species transported to non-endemic areas may potentially vector disease and genetically 'pollute' local native avifauna. To reduce the logistical difficulties associated with trafficking live birds, smugglers often transport eggs. This creates a problem for authorities in elucidating accurate species identification without the laborious task of incubation and hand rearing until a morphological identification can be made. Here, we use 99 avian eggs seized from carriers coming into and within Australia, as a result of suspected illegal trade. We investigate and evaluate the use of mitochondrial DNA (mtDNA) to accurately identify eggs to family, genus or species level. However, Identification of a species based on percentage mtDNA similarities is difficult without good representations of the inter- and intra-levels of species variation. Based on the available reference database, we were able to identify 52% of the eggs to species level. Of those, 10 species from eight genera were detected, all of which belong to the parrot (Psittacidae) and cockatoo (Cacatuidae) families. Of the remaining 48%, a further 36% of eggs were identified to genus level, and 12% identified to family level using our assignment criteria. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny.
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Affiliation(s)
- Megan L Coghlan
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, South St, Murdoch, WA 6150, Australia
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Linacre A, Gusmão L, Hecht W, Hellmann AP, Mayr WR, Parson W, Prinz M, Schneider PM, Morling N. ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 2010; 5:501-5. [PMID: 21106449 DOI: 10.1016/j.fsigen.2010.10.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
Abstract
The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.
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Affiliation(s)
- A Linacre
- School of Biology, Flinders University, Adelaide, Australia.
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A novel strategy for avian species and gender identification using the CHD gene. Mol Cell Probes 2010; 24:27-31. [DOI: 10.1016/j.mcp.2009.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 08/17/2009] [Accepted: 08/17/2009] [Indexed: 11/19/2022]
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Alacs EA, Georges A, FitzSimmons NN, Robertson J. DNA detective: a review of molecular approaches to wildlife forensics. Forensic Sci Med Pathol 2009; 6:180-94. [PMID: 20013321 DOI: 10.1007/s12024-009-9131-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2009] [Indexed: 11/26/2022]
Abstract
Illegal trade of wildlife is growing internationally and is worth more than USD$20 billion per year. DNA technologies are well suited to detect and provide evidence for cases of illicit wildlife trade yet many of the methods have not been verified for forensic applications and the diverse range of methods employed can be confusing for forensic practitioners. In this review, we describe the various genetic techniques used to provide evidence for wildlife cases and thereby exhibit the diversity of forensic questions that can be addressed using currently available genetic technologies. We emphasise that the genetic technologies to provide evidence for wildlife cases are already available, but that the research underpinning their use in forensics is lacking. Finally we advocate and encourage greater collaboration of forensic scientists with conservation geneticists to develop research programs for phylogenetic, phylogeography and population genetics studies to jointly benefit conservation and management of traded species and to provide a scientific basis for the development of forensic methods for the regulation and policing of wildlife trade.
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Affiliation(s)
- E A Alacs
- Institute for Applied Ecology and National Centre for Forensic Studies, University of Canberra, Canberra, ACT, Australia.
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Tsai LC, Lee JCI, Liao SP, Weng LH, Linacre A, Hsieh HM. Establishing the mitochondrial DNA D-loop structure of Columba livia. Electrophoresis 2009; 30:3058-3062. [DOI: 10.1002/elps.200900194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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