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Siziba VI, Scroeder MM, Wilson B, Sliwa A, Willows‐Munro S. A method for noninvasive individual genotyping of black-footed cat ( Felis nigripes). Ecol Evol 2024; 14:e11315. [PMID: 38660470 PMCID: PMC11040180 DOI: 10.1002/ece3.11315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.
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Affiliation(s)
- Vimbai I. Siziba
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | | | - Beryl Wilson
- McGregor MuseumKimberleyNorthern CapeSouth Africa
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Liang Y, Dou S, Zhao G, Shen J, Fu G, Fu L, Li S, Cong B, Dong C. Prediction of BMI traits in the Chinese population based on the gut metagenome. Microb Cell Fact 2023; 22:250. [PMID: 38066544 PMCID: PMC10704812 DOI: 10.1186/s12934-023-02255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and could serve as potential markers for forensic characterization. Previous research has established that predicting body type based on the relative abundance of the gut microbiome is relatively accurate. However, the long-term stability and high individual specificity of the gut microbiome are closely linked to changes at the genome level of the microbiome. No studies have been conducted to deduce body shape from genetic traits. Therefore, in this study, the vital role of gut bacterial community characteristics and genetic traits in predicting body mass index (BMI) was investigated using gut metagenomic data from a healthy Chinese population. RESULTS Regarding the gut microbial community, the underweight group displayed increased α-diversity in comparison to the other BMI groups. There were significant differences in the relative abundances of 19 species among these three BMI groups. The BMI prediction model, based on the 31 most significant species, showed a goodness of fit (R2) of 0.56 and a mean absolute error (MAE) of 2.09 kg/m2. The overweight group exhibited significantly higher α-diversity than the other BMI groups at the level of gut microbial genes. Furthermore, there were significant variations observed in the single-nucleotide polymorphism (SNP) density of 732 contigs between these three BMI groups. The BMI prediction model, reliant on the 62 most contributing contigs, exhibited a model R2 of 0.72 and an MAE of 1.56 kg/m2. The model predicting body type from 44 contigs correctly identified the body type of 93.55% of the study participants. CONCLUSION Based on metagenomic data from a healthy Chinese population, we demonstrated the potential of genetic traits of gut bacteria to predict an individual's BMI. The findings of this study suggest the effectiveness of a novel method for determining the body type of suspects in forensic applications using the genetic traits of the gut microbiome and holds great promise for forensic individual identification.
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Affiliation(s)
- Yu Liang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujie Dou
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangzhong Zhao
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Jie Shen
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Chunnan Dong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China.
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Ignatavičienė I, Ragauskas A, Rakauskas V, Butkauskas D. Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus. Biol Methods Protoc 2023; 8:bpad022. [PMID: 37817807 PMCID: PMC10561993 DOI: 10.1093/biomethods/bpad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples by swabbing the fish skin (including live, non-anesthetized fish) should be considered. In this study, we compared the efficiency of DNA extraction, amplification, and sequencing of mtDNA fragments of two fish species Perca fluviatilis and Rutilus rutilus based on DNA collected from the scales and mucus using the modified Aljanabi and Martinez method. The results revealed a higher quality of DNA extracted from the mucus; however, the mean DNA concentration obtained from the scales of both fish species was higher. We verified the method suitable for amplification and sequencing of mtDNA fragments of both fish species using newly designed markers (D-loop, ATP6) and examined the potential risk of intraspecific cross-contamination. The DNA sequence alignment analysis revealed identical sequences attributed to the same individual when DNA, extracted from two different sources (scales and mucus), was used. We demonstrated that the quantity and quality of DNA extracted from the scales and mucus using the proposed method were high enough to carry out genetic diversity studies based on sampling of live fish with the possibility to release it after collecting samples.
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Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
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Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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Chen Y, Sun Y, Hua M, Shi K, Dudgeon D. Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China. Integr Zool 2023; 18:453-468. [PMID: 36052971 DOI: 10.1111/1749-4877.12680] [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] [Indexed: 12/01/2022]
Abstract
A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25-32). Historic demographic contraction appeared to account for low haplotype diversity (Hd = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, He = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (FST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (FST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.
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Affiliation(s)
- Ying Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Yakuan Sun
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mei Hua
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kun Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eco-Bridge Continental, Beijing, China
| | - David Dudgeon
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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De R, Nigam P, Williams AC, Goyal SP. Beyond consensus genotyping: a case study on the Asian elephant Elephas maximus. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Kouakou JL, Gonedelé-Bi S, Assamoi JB, Assanvo N'Guetta SP. Optimization of the Cetyltrimethylammonium bromide (CTAB) DNA extraction protocol using forest elephant dung samples. MethodsX 2022; 9:101867. [PMID: 36249934 PMCID: PMC9558105 DOI: 10.1016/j.mex.2022.101867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Among non-invasive biological samples, feces offer an important source of DNA and can easily be collected. However, working with fecal DNA from highly vegetarians species such as elephant is more challenging because plant secondary compounds have an inhibitory effect on PCR reactions. Working with forest elephant dung samples, we tested and adapted a protocol of DNA extraction developed on plants based on the Cetyltrimethylammonium bromide (CTAB) protocol. The protocol is relatively simple and yields a high DNA concentration. It is five-time less expensive compared to the methods of Benbouza et al. The extracted DNA is of good quality and easily amplified by PCR. The high-amplification percentage of mitochondrial genes in fecal DNA and subsequent sequencing of PCR products indicate that the proposed optimized method is reliable for molecular analysis of forest elephant dung samples.Our optimized CTAB protocol has been adjusted by the addition of Sodium Dodecyl Sulfate (SDS) and proteinase K during the lysis phase. The combined effect of these reagents was capable of lysing cell walls and removing proteins efficiently. Moreover, the prolonged time of incubation (overnight incubation at room temperature followed by 3 hours of incubation in a water bath) enhanced the increase of DNA yield but make the optimized protocol more time-consuming.
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8
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Koitzsch KB, Anton CB, Koitzsch LO, Tjepkes TL, Schumann AC, Strasburg JL. A noninvasive and integrative approach for improving density and abundance estimates of moose. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Colby B. Anton
- Yellowstone Center for Resources, National Park Service Yellowstone National Park WY 82190 USA
| | | | - Tessa L. Tjepkes
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
| | - Abby C. Schumann
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
| | - Jared L. Strasburg
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
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9
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Identifying individual ungulates from fecal DNA: a comparison of field collection methods to maximize efficiency, ease, and success. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00176-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractNon-invasive genetic sampling can facilitate the identification of individual animals across a landscape, with applications to management and conservation. Fecal material is a readily available source of DNA, and various methods exist for collecting fecal samples for DNA preservation. In particular, swab methods offer considerable promise, but their utility in real-world field contexts remains relatively untested. We systematically compared multiple genetic fecal sampling methods across all stages of data collection and analysis, including sampling in the field, DNA extraction in the lab, and identification of individuals using microsatellite genotyping. We collected 112 fecal samples from black-tailed deer (Odocoileus hemionus columbianus) in the field in Mendocino County, California, across a range of sample conditions of unknown age. We systematically compared the efficiency, ease, and genotyping success of three methods for field collection and storage of ungulate fecal samples: whole pellets in ethanol, whole dry pellets in paper envelopes, and cotton swabs in buffer. Storage method, sample condition, and their interaction predicted genotyping success in the top binomial GLMMs. We found that swabbing pellets resulted in the greatest percentage of individually identifiable genotypes (81%, compared to 60% for dry samples and 56% for ethanol), despite lower DNA concentrations. While swabbing pellets requires a greater time investment in the field, the samples are easier and safer to store and transport, and subsequent labwork is more efficient as compared to whole-pellet collection methods. We, therefore, recommend the swab method for most contexts. We provide additional recommendations and field protocols based on subsequent collection of 2284 swab samples for a larger monitoring study of the deer population, given that this large number of samples spanned a range of sample conditions and time spent in storage.
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Shuttleworth L, Oosthuizen CJ. Comparing DNA yield from fish scales following different extraction protocols. Sci Rep 2022; 12:2836. [PMID: 35181723 PMCID: PMC8857249 DOI: 10.1038/s41598-022-06889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
Studies on genetic diversity, adaptive potential and fitness of species have become a major tool in conservation biology. These studies require biological material containing a reliable source of DNA which can be extracted and analysed. Recently, non-invasive sampling has become the preferred sampling method of such biological material; particularly when studying endangered species. Elasmoid scales from teleost fish are an example of non-invasive samples from which DNA can successfully be extracted. This study compared different extraction protocols to find an optimal method for extracting DNA from teleost fish scales. This was done with the intent to use the protocol that yielded the highest quantity of DNA on dried, archived scales. The protocols tested in this study included (1) phenol/chloroform with a TNES-urea digestion buffer, (2) phenol/chloroform with an amniocyte digestion buffer and (3) Qiagen DNeasy Blood and Tissue Kit with variations in incubation times and temperatures of each protocol. While the phenol/chloroform with TNES-urea digestion buffer yielded significantly higher concentrations of DNA compared to the other protocols, all protocols followed in this study yielded sufficient quantities of DNA for further downstream applications. Therefore, while there are multiple viable options when selecting a DNA extraction protocol, each research project’s individual needs, requirements and resources need to be carefully considered in order to choose the most effective protocol.
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Affiliation(s)
- Loraine Shuttleworth
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Carel Jakobus Oosthuizen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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11
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Stipoljev S, Safner T, Gančević P, Galov A, Stuhne T, Svetličić I, Grignolio S, Cassinello J, Šprem N. Population structure and genetic diversity of non-native aoudad populations. Sci Rep 2021; 11:12300. [PMID: 34112859 PMCID: PMC8192935 DOI: 10.1038/s41598-021-91678-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
The aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2-4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).
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Affiliation(s)
- Sunčica Stipoljev
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia
| | - Toni Safner
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia.
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000, Zagreb, Croatia.
| | - Pavao Gančević
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia
| | - Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Tina Stuhne
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia
| | - Ida Svetličić
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Stefano Grignolio
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | - Jorge Cassinello
- Estación Experimental de Zonas Áridas (EEZA-CSIC), Carretera de Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia
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Chen Y, Sun Y, Atzeni L, Gibson L, Hua M, Li K, Shi K, Dudgeon D. Anthropogenic pressures increase extinction risk of an isolated Asian elephant (Elephas maximus) population in southwestern China, as revealed by a combination of molecular- and landscape-scale approaches. Integr Zool 2021; 17:1078-1094. [PMID: 33728791 DOI: 10.1111/1749-4877.12534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Identification of the effect of anthropogenic threats on ecosystem is crucial. We used molecular tools and remote sensing to evaluate the population status of an isolated Asian elephant population in southwestern China in response to changes in habitat suitability between 1989 and 2019. A total of 22 unique genotypes were identified from 117 dung samples collected between March and June 2018 using microsatellite DNA analysis, including 13 males and 9 females. Based on the size of fecal boli, 1 animal was a juvenile, 9 were subadults, and 12 were adults, indicating that recruitment was limited. The effective population size was small (15.3) but there was no signature of a recent population bottleneck. We observed a low genetic diversity (He = 0.46 ± 0.05) and a high level of inbreeding (Fis of 0.43 ± 0.11), suggesting low population viability and high risk of extinction. In total, these elephants lost nearly two thirds (62%) of their habitat in 3 decades. The expansion of agriculture and rubber plantations followed by an increase in human settlements after 1989 increased the isolation of this population. We recommend that resettlement of 800 inhabitants of 2 villages and the abandonment of associated farmland and rubber plantations would make an additional 20 km2 of suitable habitat available. This could allow a population increase of 14 elephants, possibly by translocating individuals from elsewhere in China. Our findings can be applied to the management and conservation of other fragmented populations in China or in other range countries of Asian elephants.
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Affiliation(s)
- Ying Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yakuan Sun
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Eco-Bridge Continental, Beijing, China
| | - Luciano Atzeni
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luke Gibson
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Mei Hua
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Keyu Li
- School of Earth Sciences, Yunnan University, Kunming, China
| | - Kun Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.,Eco-Bridge Continental, Beijing, China
| | - David Dudgeon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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13
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Wimbles R, Melling LM, Cain B, Davies N, Doherty J, Johnson B, Shaw KJ. On-site genetic analysis for species identification using lab-on-a-chip. Ecol Evol 2021; 11:1535-1543. [PMID: 33613987 PMCID: PMC7882957 DOI: 10.1002/ece3.7053] [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: 11/29/2019] [Revised: 10/22/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.
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Affiliation(s)
- Ryan Wimbles
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | - Louise M. Melling
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | - Bradley Cain
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | | | | | | | - Kirsty J. Shaw
- Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
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14
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QUANTITATIVE and QUALITATIVE TEST of THE FECAL SAMPEL FROM SUMATRAN ELEPHANT (Elephas maximus sumatranus). BIOVALENTIA: BIOLOGICAL RESEARCH JOURNAL 2020. [DOI: 10.24233/biov.6.2.2020.163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sumatran Elephants (Elephas maximus sumatranus) is one of the endemic Sumatran fauna that is protected by Indonesia Law. The Remnant Forest of Acacia District Penyabungan in the landscape of Padang Sugihan is one of the elephant’s habitats in South Sumatra. Habitat degradation and fragmentation, poaching and conflicts become the major threats for the elephant population. Genetic study is one of the efforts to establish a conservation policy. It is necessary to test the quantitative and qualitative of DNA, at the extractions stage from fecal samples, in order to get the standard results on DNA concentration which will be analyzed later. The method used is through direct observation as the initial survey to determine the sampling location. Fecal samples were preserved in absolute ethanol at -20°C. The extraction process was carried out using the Quick-DNATM Fecal/Soil Microbe Miniprep Kit. Samples were tested quantitatively using a Nanodrop Thermo Scientific, with the expectation that the concentration results were considered to be 1.6-1.8 and continued with the qualitative test of DNA through electrophoresis gel agarose and UV Transilluminator. Of the 20 samples, only 12 samples showed positive results (there were DNA bands). The results of this quantitative and qualitative test could be used to determine a viable sample to be used as a product in the genetic analysis stage of Sumatran Elephants in the Remnant Forest of Acacia South Sumatra.
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Mäck K, Scharbert A, Schulz R, Sahm R. A new approach combining forensic thresholds and a multiple-tubes approach to unravel false microsatellite profiles from cross-contaminated sample material. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01175-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractContamination and degradation are known challenges for reliable genotyping, since they can cause, among other problems, false microsatellite profiles. In this study we described a method to decrease the proportion of false microsatellite profiles from fish scale samples of endangered allis shads (Alosa alosa) from a reintroduction program, where cross-contamination with DNA from other individuals and potentially degradation of samples occurred. To maximize the portion of reliably measurable results, we modified and combined two known approaches—thresholds used in forensic DNA analyses and a multiple-tubes approach. This combined approach increased reliable microsatellite profiles compared with single approaches. The forensic thresholds and the multiple-tubes approach increased the measurable results from 55 to 67% and 75%, respectively, whereas the combined approach accomplished an increase to 90%. This illustrates the potential of the combined approach for other studies with comparable problems or sample material.
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Buglione M, Petrelli S, de Filippo G, Troiano C, Rivieccio E, Notomista T, Maselli V, di Martino L, Carafa M, Gregorio R, Latini R, Fortebraccio M, Romeo G, Biliotti C, Fulgione D. Contribution to the ecology of the Italian hare (Lepus corsicanus). Sci Rep 2020; 10:13071. [PMID: 32753640 PMCID: PMC7403147 DOI: 10.1038/s41598-020-70013-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022] Open
Abstract
The Italian hare (Lepus corsicanus) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due to habitat alterations, low density and fragmented populations and ecological competition with the sympatric European hare (Lepus europaeus). Despite this status, only few and local studies have explored its ecological features. We provided some key traits of the ecological niche of the Italian hare as well as its potential distribution in the Italian peninsula. All data derived from genetically validated presences. We generated a habitat suitability model using maximum entropy distribution model for the Italian hare and its main competitor, the European hare. The dietary habits were obtained for the Italian hare with DNA metabarcoding and High-Throughput Sequencing on faecal pellets. The most relevant environmental variables affecting the potential distribution of the Italian hare are shared with the European hare, suggesting a potential competition. The variation in the observed altitudinal distribution is statistically significant between the two species.The diet of the Italian hare all year around includes 344 plant taxa accounted by 62 families. The Fagaceae, Fabaceae, Poaceae, Rosaceae and Solanaceae (counts > 20,000) represented the 90.22% of the total diet. Fabaceae (60.70%) and Fagaceae (67.47%) were the most abundant plant items occurring in the Spring/Summer and Autumn/Winter diets, respectively. The Spring/Summer diet showed richness (N = 266) and diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than the Autumn/Winter diet (N = 199, Shannon: 1.818, Evenness: 0.03096, Equitability: 0.3435). Our contribution adds important information to broaden the knowledge on the environmental (spatial and trophic) requirements of the Italian hare, representing effective support for fitting management actions in conservation planning.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Napoli, Italy
| | | | - Tommaso Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | | | - Romano Gregorio
- Cilento, Vallo di Diano e Alburni National Park, Salerno, Italy
| | - Roberta Latini
- Abruzzo, Lazio and Molise National Park, Pescasseroli, Aquila, Italy
| | | | - Giorgia Romeo
- Wildlife Section, Tuscan Regional Council, Grosseto, Italy
| | - Claudia Biliotti
- SOS Animali Onlus, Wildlife Rescue Center, Semproniano, Grosseto, Italy
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.
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Zhang M, Wei M, Dong Z, Duan H, Mao S, Feng S, Li W, Sun Z, Li J, Yan K, Liu H, Meng X, Ge H. Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment. BMC Biotechnol 2019; 19:99. [PMID: 31856784 PMCID: PMC6923993 DOI: 10.1186/s12896-019-0595-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Background To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA. Results The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor. Conclusions The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.
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Affiliation(s)
- Min Zhang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Min Wei
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China. .,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.
| | - Haibao Duan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Shuang Mao
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Senlei Feng
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Wenqian Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Zepeng Sun
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Jiawei Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Kanglu Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Hao Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Xueping Meng
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
| | - Hongxing Ge
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, Jiangsu, China
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Özkan Gülzari Ş, Jørgensen GHM, Eilertsen SM, Hansen I, Hagen SB, Fløystad I, Palme R. Measuring Faecal Glucocorticoid Metabolites to Assess Adrenocortical Activity in Reindeer. Animals (Basel) 2019; 9:ani9110987. [PMID: 31752137 PMCID: PMC6912703 DOI: 10.3390/ani9110987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
Several non-invasive methods for assessing stress responses have been developed and validated for many animal species. Due to species-specific differences in metabolism and excretion of stress hormones, methods should be validated for each species. The aim of this study was to conduct a physiological validation of an 11-oxoaetiocholanolone enzyme immunoassay (EIA) for measuring faecal cortisol metabolites (FCMs) in male reindeer by administration of adrenocorticotrophic hormone (ACTH; intramuscular, 0.25 mg per animal). A total of 317 samples were collected from eight male reindeer over a 44 h period at Tverrvatnet in Norway in mid-winter. In addition, 114 samples were collected from a group of reindeer during normal handling and calf marking at Stjernevatn in Norway. Following ACTH injection, FCM levels (median and range) were 568 (268-2415) ng/g after two hours, 2718 (414-8550) ng/g after seven hours and 918 (500-6931) ng/g after 24 h. Levels were significantly higher from seven hours onwards compared to earlier hours (p < 0.001). The FCM levels at Stjernevatn were significantly (p < 0.001) different before (samples collected zero to two hours; median: 479 ng/g) and after calf marking (eight to ten hours; median: 1469 ng/g). Identification of the faecal samples belonging to individual animals was conducted using DNA analysis across time. This study reports a successful validation of a non-invasive technique for measuring stress in reindeer, which can be applied in future studies in the fields of biology, ethology, ecology, animal conservation and welfare.
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Affiliation(s)
- Şeyda Özkan Gülzari
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
| | - Grete Helen Meisfjord Jørgensen
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
- Correspondence:
| | - Svein Morten Eilertsen
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
| | - Inger Hansen
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
| | - Snorre Bekkevold Hagen
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
| | - Ida Fløystad
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; (Ş.Ö.G.); (S.M.E.); (I.H.); (S.B.H.); (I.F.)
| | - Rupert Palme
- Department of Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria;
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Forgacs D, Wallen RL, Boedeker AL, Derr JN. Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison). BMC Genet 2019; 20:22. [PMID: 30808294 PMCID: PMC6390568 DOI: 10.1186/s12863-019-0722-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/08/2019] [Indexed: 11/25/2022] Open
Abstract
Background The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditional sources of DNA, such as blood or other tissues, few investigations have verified fecal samples as a valid source of DNA by directly comparing the results to high quality DNA samples from the same individuals. Our goal was to compare DNA from fecal and blood samples from the same 50 American plains bison (Bison bison) from Yellowstone National Park, analyze 35 short tandem repeat (STR) loci for genotyping efficiency, and compare heterozygosity estimates. Results We discovered that some of the fecal-derived genotypes obtained were significantly different from the blood-derived genotypes from the same bison. We also found that fecal-derived DNA samples often underestimated heterozygosity values, in some cases by over 20%. Conclusions These findings highlight a potential shortcoming inherent in previous wildlife studies that relied solely on a multi-tube approach, using exclusively low quality fecal DNA samples with no quality control to account for false alleles and allelic dropout. Herein, we present a rigorous marker selection protocol that is applicable for a wide range of species and report a set of 15 STR markers for use in future bison studies that yielded consistent results from both fecal and blood-derived DNA. Electronic supplementary material The online version of this article (10.1186/s12863-019-0722-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Forgacs
- Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX, 77843, USA.,Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77843, USA
| | - Rick L Wallen
- National Park Service, Yellowstone National Park, Hot Springs, Mammoth, WY, 82190, USA
| | - Amy L Boedeker
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77843, USA
| | - James N Derr
- Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX, 77843, USA. .,Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77843, USA.
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Moolman L, Morney MAD, Ferreira SM, Ganswindt A, Poole JH, Kerley GI. And Then There was One: A Camera Trap Survey of the Declining Population of African Elephants in Knysna, South Africa. AFRICAN JOURNAL OF WILDLIFE RESEARCH 2019. [DOI: 10.3957/056.049.0016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Lizette Moolman
- Scientific Services, South African National Parks, P.O. Box 3542, Knysna, 6570 South Africa
| | - Melanie A. de Morney
- Scientific Services, South African National Parks, P.O. Box 3542, Knysna, 6570 South Africa
| | - Sam M. Ferreira
- Scientific Services, South African National Parks, Private Bag X402, Skukuza, 1350 South Africa
| | - André Ganswindt
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | | | - Graham I.H. Kerley
- Centre for African Conservation Ecology, Nelson Mandela University, P.O. Box 77000, Port Elizabeth, 6031 South Africa
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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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Kim BJ, Choi TY, Park G, Lee H, Lee JM, Choi S. Morphometric analyses of non-invasive fecal samples of the Korean long-tailed goral ( Naemorhedus caudatus) for species and age identification. Anim Cells Syst (Seoul) 2018. [DOI: 10.1080/19768354.2017.1422541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Baek-Jun Kim
- Division of Basic Research, Bureau of Ecological Research, National Institute of Ecology, Chungcheongnam-do, Korea
| | - Tae-Young Choi
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Chuncheongnam-do, Korea
| | | | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Jae Min Lee
- Division of Basic Research, Bureau of Ecological Research, National Institute of Ecology, Chungcheongnam-do, Korea
| | - Sunghoon Choi
- Division of Basic Research, Bureau of Ecological Research, National Institute of Ecology, Chungcheongnam-do, Korea
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Sorokin PA, Rozhnov VV, Krasnenko AU, Lukarevskiy VS, Naidenko SV, Hernandez-Blanco JA. Genetic structure of the Amur tiger (Panthera tigris altaica) population: Are tigers in Sikhote-Alin and southwest Primorye truly isolated? Integr Zool 2016; 11:25-32. [PMID: 26663570 DOI: 10.1111/1749-4877.12175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We used molecular genetic analyses to noninvasively identify individual Amur tigers and define subpopulations of tigers in the Russian Far East. We identified 63 individuals after genotyping 256 feces, 7 hair and 11 blood samples collected within southern, central and northern Sikhote-Alin, as well as Southwest Primorye. Analysis of nuclear DNA at 9 microsatellite loci demonstrated greater genetic similarity between animals from southern and northern Sikhote-Alin (some 500 km apart) than between animals from Ussuriskii State Nature Reserve and Southwest Primorye (less than 10 km apart at their nearest point), suggesting that a true barrier exists preventing movements of tigers between Southwest Primorye and the southern Sikhote-Alin Mountains.
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Affiliation(s)
- Pavel A Sorokin
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Vyatcheslav V Rozhnov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Anna U Krasnenko
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Victor S Lukarevskiy
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Naidenko
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Jose A Hernandez-Blanco
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Timing Moose Pellet Collections to Increase Genotyping Success of Fecal DNA. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2016. [DOI: 10.3996/112015-jfwm-115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Fecal pellets can serve as a noninvasive source of DNA for identifying the distribution of individual animals when conducting population estimates. The quality of fecal DNA, however, can be degraded by wet or warm environmental conditions. We tested the effect of time of pellet collection (mid-March–mid-June) and temperature on the success of genotyping microsatellite loci in moose Alces alces by using DNA extracted from moose fecal pellets collected from north central British Columbia, Canada. Using the number of microsatellite loci genotyped as a measure of genotyping success clearly indicated that fecal pellets collected in March and April contained DNA that yielded high-confidence genotypes, whereas those collected in May and June did not. Pellets collected in March and April were more likely to be collected in cooler (often subzero) temperatures than those collected in May and June. Pellets collected later in the year were also more likely to be exposed to rain and increased solar radiation, all of which are likely to contribute to degradation of fecal DNA. Our findings suggest that pellets collected in late winter in the Northern Hemisphere have sufficient DNA to permit genotyping of moose.
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Noninvasive genetic census of greater one-horned rhinocerosRhinoceros unicornisin Gorumara National Park, India: a pilot study for population estimation. ORYX 2016. [DOI: 10.1017/s0030605314001161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AbstractThe greater one-horned rhinocerosRhinoceros unicornisis a flagship species for conservation in protected areas in India and Nepal. In India the species is afforded the highest level of legal protection under Schedule I of the Wildlife (Protection) Act 1972. Although censuses of greater one-horned rhinoceros have been carried out for decades using the traditional total count method, no advanced scientific approach has been adopted for population estimation of the species in India or elsewhere. We optimized noninvasive genetic techniques for identification of greater one-horned rhinoceros from dung samples, and applied these to estimate the number of rhinoceros in Gorumara National Park, in West Bengal, India. Our results confirmed the presence of 43 individuals from 60 dung samples collected throughout the Park in 2011. We confirmed a male-to-female sex ratio of 3.8 : 1, based on analysis of DNA from dung samples, using a y-chromosome linked marker. Our results are in concordance with a census carried out by the West Bengal Forest Department that found 42 rhinoceros in the Park, with a male-to-female sex ratio of 3.5 : 1. Our study thus demonstrates the feasibility of using a noninvasive genetic approach for population estimation of greater one-horned rhinoceros in the wild.
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Das PK, Borthakur U, Sarma HK, Talukdar BK. Population genetic assessment of extant populations of greater one-horned rhinoceros (Rhinoceros unicornis) in India. EUR J WILDLIFE RES 2015. [DOI: 10.1007/s10344-015-0960-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Hans JB, Haubner A, Arandjelovic M, Bergl RA, Fünfstück T, Gray M, Morgan DB, Robbins MM, Sanz C, Vigilant L. Characterization of MHC class II B polymorphism in multiple populations of wild gorillas using non-invasive samples and next-generation sequencing. Am J Primatol 2015; 77:1193-206. [PMID: 26283172 DOI: 10.1002/ajp.22458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/08/2015] [Accepted: 08/03/2015] [Indexed: 01/03/2023]
Abstract
Genes encoded by the major histocompatibility complex (MHC) are crucial for the recognition and presentation of antigens to the immune system. In contrast to their closest relatives, chimpanzees and humans, much less is known about variation in gorillas at these loci. This study explored the exon 2 variation of -DPB1, -DQB1, and -DRB genes in 46 gorillas from four populations while simultaneously evaluating the feasibility of using fecal samples for high-throughput MHC genotyping. By applying strict similarity- and frequency-based analysis, we found, despite our modest sample size, a total of 18 alleles that have not been described previously, thereby illustrating the potential for efficient and highly accurate MHC genotyping from non-invasive DNA samples. We emphasize the importance of controlling for multiple potential sources of error when applying this massively parallel short-read sequencing technology to PCR products generated from low concentration DNA extracts. We observed pronounced differences in MHC variation between species, subspecies and populations that are consistent with both the ancient and recent demographic histories experienced by gorillas.
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Affiliation(s)
- Jörg B Hans
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Haubner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard A Bergl
- North Carolina Zoological Park, Asheboro, North Carolina, USA
| | | | - Maryke Gray
- International Gorilla Conservation Program, Kigali, Rwanda
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Ramón-Laca A, Soriano L, Gleeson D, Godoy JA. A simple and effective method for obtaining mammal DNA from faeces. WILDLIFE BIOLOGY 2015. [DOI: 10.2981/wlb.00096] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Chandra De B, Patra MC, Kumar S, Brahma B, Goutam D, Jaiswal L, Sharma A, De S. Noninvasive method of DNA isolation from fecal epithelial tissue of dairy animals. Anim Biotechnol 2015; 26:211-6. [PMID: 25927167 DOI: 10.1080/10495398.2014.989325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A novel noninvasive genomic DNA isolation protocol from fecal tissue, by the proteinase K digestion and guanidine hydrochloride extraction method, was assessed for the genotyping of cattle and buffalo. The epithelial tissues present on the surface of the feces were used as source for isolation of genomic DNA. The DNA isolated from fecal tissue was found to be similar as those obtained from other body tissues such as skin, brain, liver, kidney, and muscle. The quality of DNA was checked by agarose gel electrophoresis and polymerase chain reaction (PCR). We successfully amplified a 320 bp MHC class II DRB gene and a 125 bp mt-DNA D-loop region from isolated genomic DNA of cattle. Thus, the DNA isolated using this method was suitable for common molecular biology methods, such as restriction enzyme digestion and genotyping of dairy animals through PCR.
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Affiliation(s)
- Bidhan Chandra De
- a National Dairy Research Institute , Animal Biotechnology Centre , Karnal , India
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31
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Harms V, Nowak C, Carl S, Muñoz-Fuentes V. Experimental evaluation of genetic predator identification from saliva traces on wildlife kills. J Mammal 2015. [DOI: 10.1093/jmammal/gyu014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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de Flamingh A, Sole CL, van Aarde RJ. Genetic evidence for spatial structuring in a continuous African elephant (Loxodonta africana) population. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0686-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Yamauchi K, Kurakake S, Morosawa T, Kondo M, Uno R, Yuasa T, Tsuruga H, Tamate HB, Yoneda M. A Pilot Study of the Hair-Trapping Method in Asiatic Black Bears (Ursus thibetanus): Determination of Optimal Survey Period for Estimating Population Size. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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How monkeys see a forest: genetic variation and population genetic structure of two forest primates. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0680-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Liu G, Zang S, Li L, Hu X, Zhao S, Li K, Hu D. Evaluation of fecal DNA preservation and extraction methods in Przewalski’s horse. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0162-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Smith O, Wang J. When can noninvasive samples provide sufficient information in conservation genetics studies? Mol Ecol Resour 2014; 14:1011-23. [PMID: 24620908 DOI: 10.1111/1755-0998.12250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
Noninvasive sampling, of faeces and hair for example, has enabled many genetic studies of wildlife populations. However, two prevailing problems common to these studies are small sample sizes and high genotyping errors. The first problem stems from the difficulty in collecting noninvasive samples, particularly from populations of rare or elusive species, and the second is caused by the low quantity and quality of DNA extracted from a noninvasive sample. A common question is therefore whether noninvasive sampling provides sufficient information for the analyses commonly conducted in conservation genetics studies. Here, we conducted a simulation study to investigate the effect of small sample sizes and genotyping errors on the precision and accuracy of the most commonly estimated genetic parameters. Our results indicate that small sample sizes cause little bias in measures of expected heterozygosity, pairwise FST and population structure, but a large downward bias in estimates of allelic diversity. Allelic dropouts and false alleles had a much smaller effect than missing data, which effectively reduces sample size further. Overall, reasonable estimates of genetic variation and population subdivision are obtainable from noninvasive samples as long as error rates are kept below a frequency of 0.2. Similarly, unbiased estimates of population clustering can be made with genotyping error rates below 0.5 when the populations are highly differentiated. These results provide a useful guide for researchers faced with studying the conservation genetics of small, endangered populations from noninvasive samples.
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Affiliation(s)
- O Smith
- Division of Biology, Imperial College London, Silwood Park, Ascot, Berks, London, SL5 7PY, UK; Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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Chakraborty S, Boominathan D, Desai AA, Vidya TNC. Using genetic analysis to estimate population size, sex ratio, and social organization in an Asian elephant population in conflict with humans in Alur, southern India. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0587-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Population size estimation of an Asian elephant population in eastern Cambodia through non-invasive mark-recapture sampling. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0579-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Müller N, Ostner J, Schülke O, Walter L. Towards the non-invasive assessment of MHC genotype in wild primates: analysis of wild Assamese macaque MHC-DRB from fecal samples. Am J Primatol 2013; 76:230-8. [PMID: 24151109 DOI: 10.1002/ajp.22225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 09/04/2013] [Accepted: 09/17/2013] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex (MHC) plays an important role in the immune response and may thus crucially affect an individual's fitness, relevant also for studies on evolutionary ecology and wildlife conservation. Detailed knowledge on the genomic organization, polymorphism and diversity of the MHC has a narrow taxonomic focus though and among macaques is only available for rhesus and long-tailed macaques-the species most commonly kept for biomedical research. The lack of data on wild populations is largely due to the difficulty of obtaining blood or tissue samples necessary for genotyping approaches. Here, we aimed at analyzing MHC-DRB from non-invasively collected fecal samples in wild Assamese macaques (Macaca assamensis), utilizing the MHC-DRB-STR (D6S2878) microsatellite marker. Due to the fecal DNA source incomplete genotypes occurred, which may be improved in the future by method refinement. We detected 28 distinct DRB-STR lengths in 43 individuals with individual genotypes containing 1-9 MHC-DRB-STRs and defined four haplotypes segregating between families in Mendelian fashion. Our results indicate that variability and diversity of MHC-DRB in Assamese macaques is comparable to that of other macaque species and importantly, that fecal samples can be used for non-invasive analysis of MHC genes after refinement of the applied methods, opening a number of opportunities for MHC research on natural populations.
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Affiliation(s)
- Nadine Müller
- Social Evolution in Primates Group, Courant Research Center Evolution of Social Behavior, Georg-August University Göttingen, Göttingen, Germany
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Hansen H, Ben-David M, McDonald DB. TECHNICAL ADVANCES: Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces. Mol Ecol Resour 2013; 8:282-9. [PMID: 21585770 DOI: 10.1111/j.1471-8286.2007.01992.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In noninvasive genetic sampling, when genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating genotyping errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two genotyping protocols (multiple-tubes and 'comparative method') in respect to genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because genotyping errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7-32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method.
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Affiliation(s)
- Heidi Hansen
- US Geological Service PIERC BRD, Kilauea Field Station, Hawaii National Park, HI 96718, USA, Department of Zoology and Physiology, University of Wyoming, 1000 E. University Avenue, Laramie, Wyoming 82071, USA
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41
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Liu G, Xu CQ, Cao Q, Zimmermann W, Songer M, Zhao SS, Li K, Hu DF. Mitochondrial and pedigree analysis in Przewalski's horse populations: implications for genetic management and reintroductions. ACTA ACUST UNITED AC 2013; 25:313-8. [PMID: 23808923 DOI: 10.3109/19401736.2013.800487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS Przewalski's horses have been imported from the western zoos to China since 1985. Yet the genetic diversity in China's populations has not been studied, thus lacking of such knowledge inevitably affects this population's management. The aim of this study was to assess genetic diversity in Chinese population of Przewalski's horses via mitochondrial DNA (mtDNA) control region and pedigree analysis. MATERIALS AND METHODS Two captive and one reintroduced populations were examined based on mitochondrial DNA control region variation via fecal sampling from 2010 to 2012, together with pedigree analysis. RESULTS Amplification success rates of fecal mtDNA were as high as 96.2% (93.8%-100%), and were higher for sample in winter than in summer and autumn. Two haplotypes were identified and shared among three populations, but the proportion of individuals with each haplotype varied among the three populations (F(ST) = 0.10874, p = 0.00978). Haplotype diversity in the released population (0.153) was much lower than that in the two captive populations (0.4011 and 0.4966), in accordance with the direction of increase in probability of identity at the dam lines. CONCLUSION Future concerns in Przewalski's horse population management should emphasize on strict reproduction control to minimize inbreeding in captivity, followed by long-term genetic diversity guidelines and non-invasive monitoring in the reintroduction programmes.
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Affiliation(s)
- Gang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Biological Science and Technology, Beijing Forestry University , Beijing , China
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42
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Rovie-Ryan JJ, Zainuddin ZZ, Marni W, Ahmad AH, Ambu LN, Payne J. Blood meal analysis of tabanid fly after it biting the rare Sumatran rhinoceros. Asian Pac J Trop Biomed 2013; 3:95-9. [PMID: 23593586 DOI: 10.1016/s2221-1691(13)60031-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 01/20/2013] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly. METHODS Blood meal was recovered from the abdomen of an engorged tabanid fly (Haematopota sp.) which was captured immediately after biting a Sumatran rhino in captivity. The blood was applied on to a Whatman FTA(®) blood card. Subsequent laboratory work was conducted to extract, amplify and sequence the DNA from the sample. Validation was done by sampling the hair follicles and blood samples from the rhinoceros and subjecting it to the same laboratory process. RESULTS BLAST search and constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. CONCLUSIONS This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases.
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Affiliation(s)
- Jeffrine Japning Rovie-Ryan
- Ex-Situ Conservation Division, Department of Wildlife and National Parks (DWNP), Peninsular Malaysia, Ministry of Natural Resources and Environment Malaysia (NRE), KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia ; Department of Zoology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300 Kota Samarahan, Sarawak, Malaysia
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43
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Simons ND, Lorenz JG, Sheeran LK, Li JH, Xia DP, Wagner RS. Noninvasive saliva collection for DNA analyses from free-ranging Tibetan macaques (Macaca thibetana). Am J Primatol 2012; 74:1064-70. [PMID: 22890787 DOI: 10.1002/ajp.22062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 06/11/2012] [Accepted: 07/02/2012] [Indexed: 11/08/2022]
Abstract
Cryptic and endangered fauna, including many primate taxa, pose challenges for noninvasive collection of biomaterials. As a result, application of noninvasive genotyping to primates has been limited to the use of samples such as feces and hair for the extraction of PCR-amplifiable DNA. We present a method for noninvasive collection of saliva from habituated, free-ranging monkeys. The method utilizes a low-cost apparatus that controls for contamination and is usable with individual, free-ranging primates. Saliva samples were collected from 18 individuals in a population of Tibetan macaques (Macaca thibetana) in the Valley of Wild Monkeys in Huangshan, People's Republic of China. DNA was extracted from these samples and PCR-amplified for both mitochondrial and nuclear genes, Cytochrome B and MHC-DR Beta 1, respectively. These results indicate this is an effective technique for the noninvasive collection of saliva across age and sex class, and dominance rank in a free-ranging, terrestrial primate species. This device could have wide application for obtaining high-quality saliva samples from free-ranging primate populations for use in epidemiological studies, hormonal analyses of HPA axis function, pathogen screening, noninvasive genotyping, and behavioral genetics.
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Affiliation(s)
- N D Simons
- Primate Behavior Program, Central Washington University, Ellensburg, Washington, USA
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RENAN SHARON, SPEYER EDITH, SHAHAR NAAMA, GUETA TOMER, TEMPLETON ALANR, BAR‐DAVID SHIRLI. A factorial design experiment as a pilot study for noninvasive genetic sampling. Mol Ecol Resour 2012; 12:1040-7. [DOI: 10.1111/j.1755-0998.2012.03170.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- SHARON RENAN
- Department of Life Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva 85104, Israel
| | - EDITH SPEYER
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - NAAMA SHAHAR
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - TOMER GUETA
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
| | - ALAN R. TEMPLETON
- Department of Biology, Washington University, St. Louis, MO 63130, USA
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa 31905, Israel
| | - SHIRLI BAR‐DAVID
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben‐Gurion University of the Negev, Sde Boqer Campus, Midreshet Ben‐Gurion 84990, Israel
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BEN LARBI M, Tircazes A, Feve K, Tudela F, Bolet G. Reliability of non-invasive tissue sampling methods for DNA extraction in rabbits (Oryctolagus cuniculus). WORLD RABBIT SCIENCE 2012. [DOI: 10.4995/wrs.2012.1077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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46
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Conserving small and fragmented populations of large mammals: Non-invasive genetic sampling in an isolated population of Asian elephants in Nepal. J Nat Conserv 2012. [DOI: 10.1016/j.jnc.2012.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Yamazaki S, Motoi Y, Nagai K, Ishinazaka T, Asano M, Suzuki M. Sex determination of sika deer (Cervus nippon yesoensis) using nested PCR from feces collected in the field. J Vet Med Sci 2011; 73:1611-6. [PMID: 21836386 DOI: 10.1292/jvms.11-0235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe a method for determining the sex of sika deer (Cervus nippon yesoensis) from feces collected in the field. Using a nested polymerase chain reaction (nested PCR), partial sequences of the sex determination region of the Y chromosome (SRY) gene and X zinc finger protein (ZFX) gene were amplified. In 19 individuals with sex information, the correct sex was successfully detected and sequences of target amplicons were completely matched between muscle and feces from the rectum. Among 75 fecal samples collected noninvasively in the field, 68-71 samples (90.7-94.7%) yielded successful sex determinations. Using this technique, feces collected in the field would enhance the utility of genetic analysis. As a result, instead of biomaterials, these samples can serve as new or alternative materials. Finally, it can be expected that this technique will contribute to reveal in advanced detail of the population dynamics and genetic diversity that needed to carry out effective population control and to reduce the extinction risk of sika deer.
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Affiliation(s)
- Shoki Yamazaki
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu 501–1193, Japan
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49
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Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-011-4634-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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50
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Macbeth GM, Broderick D, Ovenden JR, Buckworth RC. Likelihood-based genetic mark-recapture estimates when genotype samples are incomplete and contain typing errors. Theor Popul Biol 2011; 80:185-96. [PMID: 21763337 DOI: 10.1016/j.tpb.2011.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/07/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
Abstract
Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark-recapture methodology in wildlife species can therefore be prone to misidentifications leading to both 'true non-recaptures' being falsely accepted as recaptures (Type I errors) and 'true recaptures' being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standard error of recapture estimates can be minimised through our algorithms. Interestingly, the precision of our recapture estimates actually improved when we included individuals with missing genotypes, as this increased the number of pairwise comparisons potentially uncovering more recaptures. Simulations suggest that the method is tolerant to per locus error rates of up to 5% per locus and can theoretically work in datasets with as little as 60% of loci genotyped. Our methods can be implemented in datasets where standard mismatch analyses fail to distinguish recaptures. Finally, we show that by assigning a low Type I error rate to our matching algorithms we can generate a dataset of individuals of known capture histories that is suitable for the downstream analysis with traditional mark-recapture methods.
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Affiliation(s)
- Gilbert M Macbeth
- Molecular Fisheries Laboratory, Queensland Primary Industries and Fisheries, Ritchie Building No. 64A, Research Road, University of Queensland, PO Box 6097, St Lucia, Queensland, 4072, Australia.
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