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58 results for “AFLP”
Data from: One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data
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Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of datasets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error datasets and we assessed the low-error point at which expected population substructure signal was lost. In both species we identified substructure patterns deemed to be inaccurate at error rates {less than or equal to}2% and >4%. In the species comparison, the optimum datasets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.
Data from: Galega orientalis is more diverse than Galega officinalis in Caucasus – whole-genome AFLP analysis and phylogenetics of symbiosis-related genes
Legume plants can obtain combined nitrogen for their growth in an efficient way through symbiosis with specific bacteria. The symbiosis between Rhizobium galegae and its host plant Galega is an interesting case where the plant species G. orientalis and G. officinalis form effective, nitrogen fixing, symbioses only with the appropriate rhizobial counterpart, R. galegae bv. orientalis and R. galegae bv. officinalis respectively. There is plenty of information available on the symbiotic properties of nitrogen fixing rhizobia, while more information is needed on the properties of the host plants. The Caucasus region in Eurasia has been identified as the gene centre (centre of origin) of G. orientalis, although both G. orientalis and G. officinalis can be found in this region. In this study, the diversity of these two Galega species in Caucasus was investigated to test the hypothesis that in this region G. orientalis is more diverse than G. officinalis. The amplified fragment length polymorphism (AFLP) fingerprinting performed here showed that the populations of G. orientalis and R. galegae bv. orientalis are more diverse than those of G. officinalis and R. galegae bv. officinalis respectively. These results are consistent with the centre of origin status of Caucasus for G. orientalis. Phylogenies of the symbiosis-related plant genes NORK and Nfr5 were congruent with the AFLP result from a diversity point of view. Finally, the results of this work indicate that the NORK and Nfr5 genes of Galega follow the same evolutionary pattern as conserved plant genes.
Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research
Despite much discussion of the importance of quantifying and reporting genotyping error in molecular studies, it is still not standard practice in the literature. This is particularly a concern for amplified fragment length polymorphism (AFLP) studies, where differences in laboratory, peak-calling and locus-selection protocols can generate data sets varying widely in genotyping error rate, the number of loci used and potentially estimates of genetic diversity or differentiation. In our experience, papers rarely provide adequate information on AFLP reproducibility, making meaningful comparisons among studies difficult. To quantify the extent of this problem, we reviewed the current molecular ecology literature (470 recent AFLP articles) to determine the proportion of studies that report an error rate and follow established guidelines for assessing error. Fifty-four per cent of recent articles do not report any assessment of data set reproducibility. Of those studies that do claim to have assessed reproducibility, the majority (~90%) either do not report a specific error rate or do not provide sufficient details to allow the reader to judge whether error was assessed correctly. Even of the papers that do report an error rate and provide details, many (≥23%) do not follow recommended standards for quantifying error. These issues also exist for other marker types such as microsatellites, and next-generation sequencing techniques, particularly those which use restriction enzymes for fragment generation. Therefore, we urge all researchers conducting genotyping studies to estimate and more transparently report genotyping error using existing guidelines and encourage journals to enforce stricter standards for the publication of genotyping studies.
Figure 2 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 2 - AFLP Autoradiogram of pigeon pea cyst nematode Heterodera cajani with EcoRI (+AAG) + MseI, (+CAG) and EcoRI (+AAA) + MseI (CTA). Lane 1 to 11: Heterodera cajani populations from Andhra Pradesh, Allahabad, Bahadurgarh, Coimbatore, Kanpur-1, Ghaziabad, Gilberga, Hisar, Delhi, Kanpur-2, andMeja.
Figure 3 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 3 - Dendograms from cluster analysis of Heterodera cajani a) for 1278 amplified restriction fragment digests using 24 primer pairs and b) the four primer pairs that suggest a similar dendogram to the full set. The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was 3 as in both cases with realised deviates and t statistics respectively of a) 1.47 and 4.66 and b) 1.59 and 5.04.
Figure 1 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 1 - Dendograms from cluster analysis a) for the nine biometric measurements made on second stage juveniles of eleven populations of Heterodera cajani (see Table 2 for data) b) vulval cones of cysts of the same populations. (See Table 3 for data). The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was for a) 2 and for b) 3 with realized deviates and t- statistics respectively of a) 2.71 and 8.56 and b) 1.04 and 3.27.
Figure 4 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 4 - India Map showing distances of collected 11 Heterodera cajani populations with distances in (Kilometres)
Data from: Nonspecific PCR amplification by high-fidelity polymerases: implications for next-generation sequencing of AFLP markers.
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Data from: Identifying insecticide resistance genes in mosquito by combining AFLP genome scan and 454 pyrosequencing
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Data from: A call for more transparent reporting of error rates: the quality of AFLP data in ecological and evolutionary research
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Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
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Data from: Optimisation of AFLP for extremely large genomes over 70 Gb.
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Data from: Galega orientalis is more diverse than Galega officinalis in Caucasus – whole-genome AFLP analysis and phylogenetics of symbiosis-related genes
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AFLP matrix Lilium pomponium
<p>Binary AFLP fragment matrix of 20 <em>Lilium pomponium</em> populations. The primer combinations used in this preamplification were: ASII: EcoR1-AGG/ MseI -CGG, ASIII: EcoR1-AGC/ MseI -CAG, ASVII: EcoR1-AGC/ MseI -CTG dyed with 6-FAM fluorescence at 5′ Eco end. Data of populations are reported in relevé locality data table.</p>
Data from: Distribution and genetic diversity of the rare plant Veratrum woodii (Liliales: Melanthiaceae) in Georgia: a preliminary study with AFLP fingerprint data
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FIGURE 0. Paphiopedilum charlesworthii var. lannaense, A. flower, B. dorsal sepal, C. synsepal, D. petal, E. labellum, F in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE 0. Paphiopedilum charlesworthii var. lannaense, A. flower, B. dorsal sepal, C. synsepal, D. petal, E. labellum, F. staminode, column and stigma, G. leaf, H. peduncle and pedicel, I. floral bract and J. pedicel longitudinal section and transverse section (photo. by W. Tongkham)
Fig. 1 in Floral scent and its correlation with AFLP data in Sorbus
Fig. 1 Cluster analysis (UPGMA) of the scent data based on the Jaccard index of S. latifolia taxa S. adeana (plus sign), S. franconica (asterisk), and S. cordigastensis (multiplication sign) as well as their parental species
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.