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Whitlock R, Hipperson H, Mannarelli M, Butlin RK, Burke T. An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Mol Ecol Resour 2013; 8:725-35. [PMID: 21585880 DOI: 10.1111/j.1755-0998.2007.02073.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fragment locations (loci) within the fingerprint. Our method uses thresholds of AFLP-polymerase chain reaction-product fluorescence intensity (peak height) in order to: (i) exclude AFLP loci that are likely to contribute high rates of error to data sets, and (ii) determine the AFLP phenotype (fragment presence or absence) at the retained loci. Error rate analysis is an integral part of this process and is used to determine optimal thresholds that minimize genotyping error, while maximizing the numbers of retained loci. We show that application of this method to a large AFLP data set allows genotype calls that are rapid, objective and repeatable, facilitating the extraction of reliable genotype data for molecular ecological studies.
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Affiliation(s)
- R Whitlock
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Jiang XF, Cao WJ, Zhang L, Luo LZ. Beet webworm (Lepidoptera: Pyralidae) migration in China: evidence from genetic markers. ENVIRONMENTAL ENTOMOLOGY 2010; 39:232-242. [PMID: 20146861 DOI: 10.1603/en08315] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genetic diversity within and among 11 geographic populations of the beet webworm Loxostege sticticalis across five provinces in the northern part of China were evaluated using amplified fragment length polymorphism (AFLP) analysis. Five AFLP primer combinations were used on 88 L. sticticalis samples from different locations, detecting a total of 384 polymorphic and 27 monomorphic fragments. Although extensive genetic diversity occurs among individuals from different geographic populations (P = 93.4%, h = 0.398, I = 0.572), the majority of the genetic diversity is within populations and not between populations (G(ST) = 0.196), which agrees well with the results of analysis of molecular variance (84% of the total genetic variation is within populations), indicating high gene flow (N(M) = 2.046) among natural populations, which are not genetically differentiated. L. sticticalis in northeastern China, northern China, and northwestern China are part of a single large metapopulation. Cluster analyses based on AFLP data were preformed to graphically show groupings between individuals and between populations. Individuals from the same region were not grouped together very well. Eleven subpopulations were clustered into six broad groups, and there was no significant correlation between geographic distance and genetic dissimilarity (r = 0.1236, P = 0.8512). Principle component analysis also indicated a lack of genetic differentiation between the 11 populations. These results indicated that, although high genetic variability existed among individuals, there was little genetic differentiation among geographic populations, which can be explained by the effects of long distance migration of the beet webworm in China and consequent gene flow.
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Affiliation(s)
- Xing-Fu Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Alacs EA, Georges A, FitzSimmons NN, Robertson J. DNA detective: a review of molecular approaches to wildlife forensics. Forensic Sci Med Pathol 2009; 6:180-94. [PMID: 20013321 DOI: 10.1007/s12024-009-9131-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2009] [Indexed: 11/26/2022]
Abstract
Illegal trade of wildlife is growing internationally and is worth more than USD$20 billion per year. DNA technologies are well suited to detect and provide evidence for cases of illicit wildlife trade yet many of the methods have not been verified for forensic applications and the diverse range of methods employed can be confusing for forensic practitioners. In this review, we describe the various genetic techniques used to provide evidence for wildlife cases and thereby exhibit the diversity of forensic questions that can be addressed using currently available genetic technologies. We emphasise that the genetic technologies to provide evidence for wildlife cases are already available, but that the research underpinning their use in forensics is lacking. Finally we advocate and encourage greater collaboration of forensic scientists with conservation geneticists to develop research programs for phylogenetic, phylogeography and population genetics studies to jointly benefit conservation and management of traded species and to provide a scientific basis for the development of forensic methods for the regulation and policing of wildlife trade.
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Affiliation(s)
- E A Alacs
- Institute for Applied Ecology and National Centre for Forensic Studies, University of Canberra, Canberra, ACT, Australia.
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WHITLOCK R, HIPPERSON H, MANNARELLI M, BUTLIN RK, BURKE T. An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Mol Ecol Resour 2008. [DOI: 10.1111/j.1471-8286.2007.02073.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kadota K, Araki R, Nakai Y, Abe M. GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data. Algorithms Mol Biol 2007; 2:5. [PMID: 17535446 PMCID: PMC1904450 DOI: 10.1186/1748-7188-2-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 05/30/2007] [Indexed: 11/28/2022] Open
Abstract
Background One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived fragments (TDFs). However, high-throughput analysis of the cDNA-AFLP data is currently limited by the need for labor-intensive visual evaluation of multiple electropherograms. We would like to have high-throughput ways of identifying such TDFs. Results We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party. Conclusion GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.
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Affiliation(s)
- Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryoko Araki
- Transcriptome Research Center, National Institute of Radiological Sciences (NIRS), 9-1, Anagawa-4-chome, Chiba-shi 263-8555, Japan
| | - Yuji Nakai
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masumi Abe
- Transcriptome Research Center, National Institute of Radiological Sciences (NIRS), 9-1, Anagawa-4-chome, Chiba-shi 263-8555, Japan
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Chang A, Liew WC, Chuah A, Lim Z, Lin Q, Orban L. FluoMEP: a new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism. Electrophoresis 2007; 28:525-34. [PMID: 17304486 DOI: 10.1002/elps.200600715] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
PCR-based identification of differences between two unknown genomes often requires complex manipulation of the templates prior to amplification and/or gel electrophoretic separation of a large number of samples with manual methods. Here, we describe a new genotyping method, called fluorescent motif enhanced polymorphism (fluoMEP). The fluoMEP method is based on random amplified polymorphic DNA (RAPD) assay, but combines the advantages of the large collection of unlabelled 10mer primers (ca. 5000) from commercial sources and the power of the automated CE devices used for the detection of amplified fragment length polymorphism (AFLP) patterns. The link between these two components is provided by a fluorescently labeled "common primer" that is used in a two-primer PCR together with an unlabeled RAPD primer. By using the same "common primer" and a series of RAPD primers, DNA templates can be screened quickly and effectively for polymorphisms. Our manuscript describes the optimization of the method and its characterization on different templates. We demonstrate by using several different approaches that the addition of the "common primer" to the PCR changes the profile of amplified fragments, allowing for screening various parts of the genome with the same set of unlabeled primers. We also present an in silico analysis of the genomic localization of fragments amplified by a RAPD primer with two different "common primers" and alone.
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Affiliation(s)
- Alex Chang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
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Abstract
The 500-1000 cichlid species endemic to Lake Malawi constitute one of the most rapid and extensive radiations of vertebrates known. There is a growing debate over the role natural and sexual selection have played in creating this remarkable assemblage of species. Phylogenetic analysis of the Lake Malawi species flock has been confounded by the lack of appropriate morphological characters and an exceptional rate of speciation, which has allowed ancestral molecular polymorphisms to persist within species. To overcome this problem we used amplified fragment length polymorphism (AFLP) to reconstruct the evolution of species within three genera of Lake Malawi sand-dwelling cichlids that construct elaborate male display platforms, or bowers. Sister taxa with distinct bower morphologies, and that exist in discrete leks separated by only 1-2 m of depth, are divergent in both sexually selected and ecological traits. Our phylogeny suggests that the forces of sexual and ecological selection are intertwined during the speciation of this group and that specific bower characteristics and trophic morphologies have evolved repeatedly. These results suggest that trophic morphology and bower form may be inappropriate characters for delineating taxonomic lineages. Specifically the morphological characters used to describe the genera Lethrinops and Tramitichromis do not define monophyletic clades. Using a combination of behavioural and genetic characters, we were able to identify several cryptic cichlid species on a single beach, which suggests that sand dweller species richness has been severely underestimated.
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Affiliation(s)
- Michael R Kidd
- Hubbard Center for Genome Studies and Department of Zoology, Suite 400, Gregg Hall, 35 Colovos Road, University of New Hampshire, Durham, NH 03824, USA.
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Stakenborg T, Vicca J, Butaye P, Maes D, Peeters J, de Kruif A, Haesebrouck F. The diversity of Mycoplasma hyopneumoniae within and between herds using pulsed-field gel electrophoresis. Vet Microbiol 2005; 109:29-36. [PMID: 15963665 DOI: 10.1016/j.vetmic.2005.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 05/09/2005] [Accepted: 05/12/2005] [Indexed: 10/25/2022]
Abstract
Over the years, pulsed-field gel electrophoresis (PFGE) has been proven a robust technique to type isolates with a high resolution and a good reproducibility. In this study, a PFGE protocol is described for the typing of Mycoplasma hyopneumoniae isolates. The potential of this technique was demonstrated by comparing M. hyopneumoniae isolates obtained from the same as well as from different herds. The use of two different restriction enzymes, SalI and ApaI, was evaluated. For each enzyme, the resulting restriction profiles were clustered using the unweighted pair group method with arithmetic means (UPGMA). For both obtained dendrograms, the included isolates of the related M. flocculare species clustered separately from all M. hyopneumoniae isolates, forming the root of the dendrograms. The PFGE patterns of the M. hyopneumoniae isolates of different herds were highly diverse and clustered differently in both dendrograms, illustrated by a Pearson's correlation coefficient of only 0.33. A much higher similarity was observed with isolates originating from different pigs of a same herd. The PFGE patterns of these isolates always clustered according to their herd and this for both dendrograms. In conclusion, the results indicate a closer relationship of M. hyopneumoniae isolates within a herd compared to isolates from different herds and this for both restriction enzymes used. Since the described PFGE technique was shown to be highly discriminative and reproducible, it will be a helpful tool to further elucidate the epidemiology of M. hyopneumoniae.
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Affiliation(s)
- Tim Stakenborg
- Veterinary and Agrochemical Research Centre, Groeselenberg 99, 1180 Brussels, Belgium.
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Terzi V, Morcia C, Giovanardi D, D’Egidio MG, Stanca AM, Faccioli P. DNA-based analysis for authenticity assessment of monovarietal pasta. Eur Food Res Technol 2004. [DOI: 10.1007/s00217-004-0965-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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