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Niimura Y, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T. Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Mol Biol Evol 2024; 41:msae071. [PMID: 38649162 PMCID: PMC11035023 DOI: 10.1093/molbev/msae071] [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: 02/02/2023] [Revised: 02/02/2024] [Accepted: 03/03/2024] [Indexed: 04/25/2024] Open
Abstract
Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.
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Affiliation(s)
- Yoshihito Niimura
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Bhim B Biswa
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
| | - Takushi Kishida
- Curatorial Division, Museum of Natural and Environmental History, Shizuoka, Japan
- Present address: College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
| | - Masato Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Scott H Jenkins
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Present address: Biosphere Informatics Laboratory, Department of Social Informatics, Graduate School of Informatics, Kyoto, Japan
| | - Christopher Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Boniface B Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
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Coetzer WG. A phylogeographic assessment of South African greater cane rats (Thryonomys swinderianus): Preliminary insights. VERTEBRATE ZOOLOGY 2023. [DOI: 10.3897/vz.73.e94111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The greater cane rat (Thryonomys swinderianus) is an African rodent with a wide Sub-Saharan distribution range. This species is viewed as an important protein source in many African countries. These rodents are also regularly viewed as a pest species who frequently raid croplands in agricultural settings. No phylogenetic work has to date been published on T. swinderianus from southern Africa. This paper therefore reports the first phylogenetic assessment on the species across the South African distribution range. Thirty samples were sourced from local museum collections, with one direct submission by a member of the public who found a rodent carcass identified as T. swinderianus west of its known distribution range in the Eastern Cape Province of South Africa. Two mitochondrial loci previously used in West African studies of this species were used in the current study to asses T. swinderianus population genetic diversity and phylogenetic structure across the South African distribution. A comparison to sequence data from West Africa was also performed. A divergence time estimation was conducted to further investigate the evolutionary history of the South African sub-population. Similar genetic diversity estimates were observed for the South African sub-population when compared to the West African datasets. Specimens from the eastern parts of South Africa showed higher genetic diversity estimates, possibly indicative of an initial colonisation site from eastern Africa. Two distinct phylogenetic clades were identified by Bayesian inference, forming distinct West African and South African groups. The divergence estimates showed similar ages for the T. swinderianus most recent common ancestor (MRCA) as previously reported. The MRCA estimates for the South African group identified a possible middle to late Pleistocene migratory event from eastern African into southern Africa. Further fine scale sampling across the African distribution range is however needed to provide more accurate assessments for future conservation management planning for the different sub-populations, as needed.
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Bacterial and protozoan pathogens/symbionts in ticks infecting wild grasscutters (Thryonomys swinderianus) in Ghana. Acta Trop 2020; 205:105388. [PMID: 32035054 DOI: 10.1016/j.actatropica.2020.105388] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 12/20/2022]
Abstract
Ticks and tick-borne pathogens constitute a great threat to livestock production and are a potential health hazard to humans. Grasscutters (Thryonomys swinderianus) are widely hunted for meat in Ghana and many other West and Central African countries. However, tick-borne zoonotic risks posed by wild grasscutters have not been assessed. The objective of this study was to investigate bacterial and protozoan pathogens in ticks infecting wild grasscutters. A total of 81 ticks were collected from three hunted grasscutters purchased from Kantamanto, the central bushmeat market in Accra. Ticks were identified as Ixodes aulacodi and Rhipicephalus sp. based on morphological keys, which were further confirmed by sequencing mitochondrial 16S ribosomal DNA (rDNA) and cytochrome oxidase I (COI) genes of specimens. Protozoan infections were tested by PCR amplifying 18S rDNA of Babesia/Theileria/Hepatozoon, while bacterial infections were evaluated by PCRs or real-time PCRs targeting Anaplasmataceae, Borrelia, spotted fever group rickettsiae, chlamydiae and Candidatus Midichloria mitochondrii. The results of PCR screening showed that 35.5% (27 out of 76) of I. aulacodi were positive for parasite infections. Sequencing analysis of the amplified products gave one identical sequence showing similarity with Babesia spp. reported from Africa. The Ca. M. mitochondrii endosymbiont was present in 85.5% (65 out of 76) of I. aulacodi but not in the five Rhipicephalus ticks. Two Anaplasmataceae bacteria genetically related to Ehrlichia muris and Anaplasma phagocytophilum were also detected in two I. aulacodi. None of the ticks were positive for Borrelia spp., spotted fever group rickettsiae and chlamydiae. Since I. aulacodi on wild grasscutters are potential carriers of tick-borne pathogens, some of which could be of zoonotic potential, rigorous tick control and pathogen analyses should be instituted especially when wild caught grasscutters are being used as foundation stock for breeding.
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Mustapha OA, Teriba EE, Ezekiel OS, Olude AM, Akinloye AK, Olopade JO. A study of scientific publications on the greater cane rat ( Thryonomys swinderianus, Temminck 1827). Animal Model Exp Med 2020; 3:40-46. [PMID: 32318658 PMCID: PMC7167232 DOI: 10.1002/ame2.12103] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/18/2019] [Accepted: 02/07/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The greater cane rat (GCR), reputed to be African's second largest rodent, is a precocial hystricomorph with an uncommon phenotype and life history. Scientific and socio-economic interests in the GCR have led to heightened research efforts targeted towards a better understanding of its biology and exploration of its economic and translational usefulness. METHODS Records of all online scientific publications on the GCR from Google, Google Scholar, PubMed, science.gov, Ebscohost and Worldwide science, with the exception of research theses, proceedings, unpublished projects and abstracts, were collated and analyzed using descriptive statistics. RESULTS A total of 146 published scholarly articles spanning about six decades were retrieved, with 98% of the GCR publications originating from African countries. Nigeria boasts the highest number of publications (58.22%) followed by Ghana (21.23%) and South Africa (5.48%) while Senegal contributed the least (0.69%). Publications were sorted into ten field categories. The field with the highest number of articles (41.78%) was animal breeding and management recording, closely followed by anatomy (37.67%). Lesser contributions were made by parasitology (5.48%), biochemistry/hematology (4.8%), pharmacology/toxicology (4.11%), pathology (2.06%), and surgery/anesthesia and physiology (1.37% apiece). The fields with fewest contributions were microbiology and developmental biology (0.69% each). CONCLUSION This study chronicles the spectrum of knowledge available on the GCR, highlighting the knowledge gap that still exists in various fields in order to provide advocacy for new frontiers in research efforts on this rodent. We suggest the need for a clearly defined and well integrated national/regional policy aimed at establishing Africa's foremost micro-livestock rodent, the greater cane rat, on the world's scientific radar.
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Affiliation(s)
- Oluwaseun Ahmed Mustapha
- Department of Veterinary AnatomyCollege of Veterinary MedicineFederal University of AgricultureAbeokutaNigeria
- Department of Veterinary AnatomyFaculty of Veterinary MedicineUniversity of IbadanIbadanNigeria
| | - Ebunoluwa Elizabeth Teriba
- Department of Veterinary AnatomyCollege of Veterinary MedicineFederal University of AgricultureAbeokutaNigeria
| | - Oluwaseun Samuel Ezekiel
- Department of Veterinary AnatomyCollege of Veterinary MedicineFederal University of AgricultureAbeokutaNigeria
| | - Ayokunle Matthew Olude
- Department of Veterinary AnatomyCollege of Veterinary MedicineFederal University of AgricultureAbeokutaNigeria
- Department of Animal Production and HealthFederal University of Technology AkureAkureNigeria
| | - Adebayo Koyuum Akinloye
- Department of Veterinary AnatomyCollege of Veterinary MedicineFederal University of AgricultureAbeokutaNigeria
| | - James Olukayode Olopade
- Department of Veterinary AnatomyFaculty of Veterinary MedicineUniversity of IbadanIbadanNigeria
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Kawasaki K, Ohya K, Omatsu T, Katayama Y, Takashima Y, Kinoshita T, Odoi JO, Sawai K, Fukushi H, Ogawa H, Inoue-Murayama M, Mizutani T, Adenyo C, Matsumoto Y, Kayang B. Comparative Analysis of Fecal Microbiota in Grasscutter ( Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana. Microorganisms 2020; 8:microorganisms8020265. [PMID: 32075341 PMCID: PMC7074823 DOI: 10.3390/microorganisms8020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022] Open
Abstract
The grasscutter (also known as the greater cane rat; Thryonomys swinderianus) is a large rodent native to West Africa that is currently under domestication process for meat production. However, little is known about the physiology of this species. In the present study, aiming to provide information about gut microbiota of the grasscutter and better understand its physiology, we investigated the intestinal microbiota of grasscutters and compared it with that of other livestock (cattle, goat, rabbit, and sheep) using 16S rRNA metagenomics analysis. Similar to the other herbivorous animals, bacteria classified as Bacteroidales, Clostridiales, Ruminococcaceae, and Lachnospiraceae were abundant in the microbiome of grasscutters. However, Prevotella and Treponema bacteria, which have fiber fermentation ability, were especially abundant in grasscutters, where the relative abundance of these genera was higher than that in the other animals. The presence of these genera might confer grasscutters the ability to easily breakdown dietary fibers. Diets for grasscutters should be made from ingredients not consumed by humans to avoid competition for resources and the ability to digest fibers may allow the use of fiber-rich feed materials not used by humans. Our findings serve as reference and support future studies on changes in the gut microbiota of the grasscutter as domestication progresses in order to establish appropriate feeding methods and captivity conditions.
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Affiliation(s)
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1112, Japan
- Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1112, Japan
| | - Tsutomu Omatsu
- Faculty of Agriculture, Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Yukie Katayama
- Faculty of Agriculture, Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Yasuhiro Takashima
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1112, Japan
- Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1112, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193, Japan
| | | | - Justice Opare Odoi
- Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1112, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1112, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1112, Japan
- Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1112, Japan
| | - Hirohito Ogawa
- Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama 700-0914, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan
- Wildlife Genome Collaborative Research Group, National Institute of Environmental Studies, Tsukuba 305-8506, Japan
| | - Tetsuya Mizutani
- Faculty of Agriculture, Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Christopher Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 38, Ghana
| | - Yoshiki Matsumoto
- Faculty of Agriculture, Kagawa University, Kagawa 761-0795, Japan
- Correspondence: (Y.M.); (B.K.); Tel.: +81-87-891-3057 (Y.M.)
| | - Boniface Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 226, Ghana
- Correspondence: (Y.M.); (B.K.); Tel.: +81-87-891-3057 (Y.M.)
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Joshi R, Árnyasi M, Lien S, Gjøen HM, Alvarez AT, Kent M. Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia ( O. niloticus). Front Genet 2018; 9:472. [PMID: 30374365 PMCID: PMC6196754 DOI: 10.3389/fgene.2018.00472] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/24/2018] [Indexed: 11/22/2022] Open
Abstract
Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.
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Affiliation(s)
- Rajesh Joshi
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Hans Magnus Gjøen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Matthew Kent
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Bourgeois S, Senn H, Kaden J, Taggart JB, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K, McEwing R. Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant. Ecol Evol 2018; 8:2207-2217. [PMID: 29468037 PMCID: PMC5817121 DOI: 10.1002/ece3.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs NationauxLibrevilleGabon
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Helen Senn
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - Jenny Kaden
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - John B. Taggart
- Aquaculture Pathfoot BuildingUniversity of StirlingStirlingUK
| | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies & The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs NationauxLibrevilleGabon
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
| | - Nils Bunnefeld
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Katharine Abernethy
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
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Coker OM, Omonona AO, Fagbohun OA, Pylant C, Austin JD. Genetic structure of wild and domesticated grasscutters (Thryonomys swinderianus) from south-western Nigeria. AFRICAN ZOOLOGY 2017. [DOI: 10.1080/15627020.2017.1379358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Oluwakayode M Coker
- Department of Wildlife and Ecotourism Management, University of Ibadan, Ibadan, Nigeria
| | - Abosede O Omonona
- Department of Wildlife and Ecotourism Management, University of Ibadan, Ibadan, Nigeria
| | - Olusegun A Fagbohun
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
| | - Cortney Pylant
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
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