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Prado NA, Armstrong EE, Brown JL, Goldenberg SZ, Leimgruber P, Pearson VR, Maldonado JE, Campana MG. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research. J Hered 2023; 114:529-538. [PMID: 37246890 DOI: 10.1093/jhered/esad034] [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: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.
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Affiliation(s)
- Natalia A Prado
- Biology Department, College of Arts and Sciences, Adelphi University, Garden City, NY, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA, United States
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janine L Brown
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Shifra Z Goldenberg
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Peter Leimgruber
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Virginia R Pearson
- Glenn Rall Laboratory, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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2
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Al Rawahi Q, Mijangos JL, Khatkar MS, Al Abri MA, AlJahdhami MH, Kaden J, Senn H, Brittain K, Gongora J. Rescued back from extinction in the wild: past, present and future of the genetics of the Arabian oryx in Oman. ROYAL SOCIETY OPEN SCIENCE 2022; 9:210558. [PMID: 35308631 PMCID: PMC8924751 DOI: 10.1098/rsos.210558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the 'World Herd', established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx. Individuals from the 'World Herd' and the United Arab Emirates have been the main source for the WWR programme. However, no breeding strategies accounting for genetic diversity have been implemented. To address this, we investigated the diversity of the WWR population and historical samples using mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs). We found individuals at WWR contain 58% of the total mtDNA diversity observed globally. Inference of ancestry and spatial patterns of SNP variation shows the presence of three ancestral sources and three different groups of individuals. Similar levels of diversity and low inbreeding were observed between groups. We identified individuals and groups that could most effectively contribute to maximizing genetic diversity. Our results will be valuable to guide breeding and reintroduction programmes at WWR.
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Affiliation(s)
- Qais Al Rawahi
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Office for Conservation of the Environment, Diwan of Royal Court, PO Box 246, P.C. 100, Muscat, Oman
- College of Applied Sciences, A'Sharqiyah University, PO Box 42, Postal Code 400, Ibra, Sultanate of Oman
| | - Jose Luis Mijangos
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Mehar S. Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mohammed A. Al Abri
- Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mansoor H. AlJahdhami
- Office for Conservation of the Environment, Diwan of Royal Court, PO Box 246, P.C. 100, Muscat, Oman
| | - Jennifer Kaden
- RZSSWildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Helen Senn
- RZSSWildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Katherine Brittain
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
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3
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Gooley RM, Dicks KL, Ferrie GM, Lacy RC, Ballou JD, Callicrate T, Senn H, Koepfli KP, Edwards CW, Pukazhenthi BS. Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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4
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Nationwide abundance and distribution of African forest elephants across Gabon using non-invasive SNP genotyping. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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5
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Athira TK, Vidya TNC. Elephant Social Systems: What Do We Know and How Have Molecular Tools Helped? J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Laguardia A, Gobush K, Bourgeois S, Strindberg S, Abitsi G, Ebouta F, Fay J, Gopalaswamy A, Maisels F, Ogden R, White L, Stokes E. Assessing the feasibility of density estimation methodologies for African forest elephant at large spatial scales. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Marasinghe MSLRP, Nilanthi RMR, Hathurusinghe HABM, Sooriyabandara MGC, Chandrasekara CHWMRB, Jayawardana KANC, Kodagoda MM, Rajapakse RC, Bandaranayake PCG. Revisiting traditional SSR based methodologies available for elephant genetic studies. Sci Rep 2021; 11:8718. [PMID: 33888797 PMCID: PMC8062488 DOI: 10.1038/s41598-021-88034-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.
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Affiliation(s)
- M S L R P Marasinghe
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - R M R Nilanthi
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - H A B M Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - M G C Sooriyabandara
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - C H W M R B Chandrasekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - K A N C Jayawardana
- Department of Wildlife Conservation, 811/A, Jayanthipura Road, Battaramulla, 10120, Sri Lanka
| | - M M Kodagoda
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - R C Rajapakse
- Department of National Zoological Gardens, Anagarika Dharmapala Mawatha, Dehiwala, 10350, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
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Magliolo M, Prost S, Orozco-terWengel P, Burger P, Kropff AS, Kotze A, Grobler JP, Dalton DL. Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus). Mol Biol Rep 2020; 48:171-181. [PMID: 33275194 DOI: 10.1007/s11033-020-06030-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.
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Affiliation(s)
- Michelle Magliolo
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Stefan Prost
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Nature Research Society, Frankfurt, Germany
| | | | - Pamela Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Anna S Kropff
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
| | - Antoinette Kotze
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desire Lee Dalton
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa. .,Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
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O'Toole B, Simmons NB, Hekkala E. Reconstructing the Genomic Diversity of a Widespread Sub-Saharan Bat (Pteropodidae: Eidolon helvum) Using Archival Museum Collections. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Brian O'Toole
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
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10
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Ross S, Costanzi JM, Al Jahdhami M, Al Rawahi H, Ghazali M, Senn H. First evaluation of the population structure, genetic diversity and landscape connectivity of the Endangered Arabian tahr. Mamm Biol 2020; 100:659-673. [PMID: 33192220 PMCID: PMC7661410 DOI: 10.1007/s42991-020-00072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022]
Abstract
The Arabian tahr (Arabitragus jayakari) occurs only in the mountains of northern Oman and the United Arab Emirates. The species is classified as Endangered due to its small declining population. In this study, we combined genetic and landscape ecology techniques in order to inform landscape scale conservation and genetic management of Arabian tahr. Using 540 base pairs of mitochondrial control region in a dataset of 53 samples, we found eight haplotypes, which fell into two haplogroups. Population genetic analysis using a panel of 14 microsatellite loci also showed a weak, but significant division. Analyses of landscape connectivity supported the genetic results showing poor connectivity between populations in the far south of the study area and those in the north. The most likely location of corridors connecting Arabian tahr populations were identified. Many corridors between tahr populations are impeded by multi-lane highways and restoration of these connections is required to maintain population viability of Arabian tahr. Owing to limited genetic samples outside of Wadi Sareen, further sampling is needed to elucidate both mtDNA and the nuclear structure of Arabian tahr more fully. Our study provides a toolkit that may be used for future genetic and connectivity monitoring of the Arabian tahr population.
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Affiliation(s)
- Steven Ross
- Office for Conservation of the Environment, Diwan of Royal Court, P.O. Box 246, 100 Muscat, Sultanate of Oman
| | - Jean-Marc Costanzi
- WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, EH12 6TS UK
| | - Mansoor Al Jahdhami
- Office for Conservation of the Environment, Diwan of Royal Court, P.O. Box 246, 100 Muscat, Sultanate of Oman
| | - Haitham Al Rawahi
- Office for Conservation of the Environment, Diwan of Royal Court, P.O. Box 246, 100 Muscat, Sultanate of Oman
| | - Muhammad Ghazali
- WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, EH12 6TS UK
| | - Helen Senn
- WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, EH12 6TS UK
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11
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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12
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Wosula EN, Chen W, Amour M, Fei Z, Legg JP. KASP Genotyping as a Molecular Tool for Diagnosis of Cassava-Colonizing Bemisia tabaci. INSECTS 2020; 11:insects11050305. [PMID: 32423055 PMCID: PMC7290743 DOI: 10.3390/insects11050305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Bemisia tabaci is a cryptic species complex that requires the use of molecular tools for identification. The most widely used approach for achieving this is the partial sequencing of the mitochondrial DNA cytochrome oxidase I gene (COI). A more reliable single nucleotide polymorphism (SNP)-based genotyping approach, using Nextera restriction-site-associated DNA (NextRAD) sequencing, has demonstrated the existence of six major haplogroups of B. tabaci on cassava in Africa. However, NextRAD sequencing is costly and time-consuming. We, therefore, developed a cheaper and more rapid diagnostic using the Kompetitive Allele-Specific PCR (KASP) approach. Seven sets of primers were designed to distinguish the six B. tabaci haplogroups based on the NextRAD data. Out of the 152 whitefly samples that were tested using these primer sets, 151 (99.3%) produced genotyping results consistent with NextRAD. The KASP assay was designed using NextRAD data on whiteflies from cassava in 18 countries across sub-Saharan Africa. This assay can, therefore, be routinely used to rapidly diagnose cassava B. tabaci by laboratories that are researching or monitoring this pest in Africa. This is the first study to develop an SNP-based assay to distinguish B. tabaci whiteflies on cassava in Africa, and the first application of the KASP technique for insect identification.
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Affiliation(s)
- Everlyne N. Wosula
- International Institute of Tropical Agriculture, P.O. Box 34441 Dar es Salaa, Tanzania; (M.A.); (J.P.L.)
- Correspondence: ; Tel.: +255-22-2700-092
| | - Wenbo Chen
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA; (W.C.); (Z.F.)
| | - Massoud Amour
- International Institute of Tropical Agriculture, P.O. Box 34441 Dar es Salaa, Tanzania; (M.A.); (J.P.L.)
| | - Zhangjun Fei
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA; (W.C.); (Z.F.)
- USDA-ARS Robert W. Holley Center for Agriculture and Health, 533 Tower Rd, Ithaca, NY 14853, USA
| | - James P. Legg
- International Institute of Tropical Agriculture, P.O. Box 34441 Dar es Salaa, Tanzania; (M.A.); (J.P.L.)
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Senn HV, Ghazali M, Kaden J, Barclay D, Harrower B, Campbell RD, Macdonald DW, Kitchener AC. Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration. Evol Appl 2019; 12:399-414. [PMID: 30828363 PMCID: PMC6383845 DOI: 10.1111/eva.12720] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/15/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.
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Affiliation(s)
- Helen V. Senn
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Jennifer Kaden
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - David Barclay
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Ben Harrower
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | | | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology, Recanati Kaplan Centre, Zoology DepartmentOxford UniversityOxfordUK
| | - Andrew C. Kitchener
- Department Natural SciencesNational Museums ScotlandEdinburghUK
- Institute of Geography, School of GeosciencesUniversity of EdinburghEdinburghUK
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Bourgeois S, Kaden J, Senn H, Bunnefeld N, Jeffery KJ, Akomo-Okoue EF, Ogden R, McEwing R. Improving cost-efficiency of faecal genotyping: New tools for elephant species. PLoS One 2019; 14:e0210811. [PMID: 30699177 PMCID: PMC6353156 DOI: 10.1371/journal.pone.0210811] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022] Open
Abstract
Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- * E-mail:
| | - Jenny Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Helen Senn
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Nils Bunnefeld
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Institut de Recherche en Écologie Tropicale, Libreville, Gabon
| | | | - Rob Ogden
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
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RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding. G3-GENES GENOMES GENETICS 2018; 8:2709-2722. [PMID: 29954843 PMCID: PMC6071602 DOI: 10.1534/g3.118.200171] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.
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