An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error

Whitlock, Raj; Hipperson, Helen; Mannarelli, Maria‐Elena; BUTLIN, R. K.; Burke, Terry

doi:10.1111/j.1471-8286.2007.02073.x

Cited by 61 publications

(91 citation statements)

References 20 publications

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“…Size and peak height of fragments between 100 and 500 bp were determined using GeneMapper v.3.7 (Applied Biosystems). Bins were checked by eye and preprocessed for threshold optimization for locus retention and phenotype calling with AFLP-SCORE 1.4a (Whitlock et al, 2008) following (Mattersdorfer et al, 2012). The average mismatch error rate was 1.26%.…”

Section: Samples and Molecular Techniquesmentioning

confidence: 99%

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

et al. 2016

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In Lake Tanganyika, lake level fluctuations were shown to have had a major impact on the evolution of littoral species. Many species are subdivided into arrays of populations, geographical races and sister species, each colonizing a particular section of the shore. Their often limited dispersal abilities promoted geographic isolation and, on the long run, allopatric speciation. With more than 120 distinct populations, the genus Tropheus represents the most spectacular and best-studied example of this phenomenon. The present study aims at the fine-scale reconstruction of the spread of two mitochondrial Tropheus-lineages in the very north of the lake, where two species, T. sp. 'black' and T. brichardi, occur. Using mtDNA sequences and AFLP-data, we analyzed samples from 21 localities and found a highly complex conglomerate of introgressed populations formed by the repeated contact of two lineages. Our data suggest repeated cross-lake dispersal of T. sp. 'black' haplotypes along the ridge between the West and East Ubwari Fault, supporting an additional persisting lowstand-lake in the Bujumbura subbasin at the very north of the lake and highlighting once more the impact of lake level fluctuations on the genetic structure and evolution of stenotopic rockdwelling cichlid species.

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Section: Samples and Molecular Techniquesmentioning

confidence: 99%

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

et al. 2016

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“…Error rates e 1 and e 2 are, respectively, the probability of mis-scoring either a '1' allele or a '0' allele. The initial and final numbers of loci refer to the initial number of fragment length classes (bins) considered, and the final number of loci retained for analysis after scoring via AFLPSCORE (Whitlock et al, 2008b). The number of replicates refers to the number of replicate pairs of fingerprints from which genotyping error was estimated.…”

Section: Outlier Analysesmentioning

confidence: 99%

“…Nomenclature for AFLP scoring thresholds follows Whitlock et al (2008b), and these are given as values of relative fluorescence units. Error rates e 1 and e 2 are, respectively, the probability of mis-scoring either a '1' allele or a '0' allele.…”

Section: Outlier Analysesmentioning

confidence: 99%

“…First, sets of fragment length classes (bins) of width 1 base pair were created for each primer combination in the interval 50-500 base pairs. Next GENEMAPPER was used to (Hadfield et al, 2006;Whitlock et al, 2008b). In total (across all six AFLP primer combinations), 191 AFLP loci were scored (of which 183 were polymorphic in the study as a whole) for each individual of S. hermonthica.…”

Section: Dna Extractionmentioning

confidence: 99%

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Variation for host range within and among populations of the parasitic plant Striga hermonthica

et al. 2011

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Striga hermonthica is an angiosperm parasite that causes substantial damage to a wide variety of cereal crop species, and to the livelihoods of subsistence farmers in sub-Saharan Africa. The broad host range of this parasite makes it a fascinating model for the study of host-parasite interactions, and suggests that effective long-term control strategies for the parasite will require an understanding of the potential for host range adaptation in parasite populations. We used a controlled experiment to test the extent to which the success or failure of S. hermonthica parasites to develop on a particular host cultivar (host resistance/compatibility) depends upon the identity of interacting host genotypes and parasite populations. We also tested the hypothesis that there is a genetic component to host range within individual S. hermonthica populations, using three rice cultivars with known, contrasting abilities to resist infection. The developmental success of S. hermonthica parasites growing on different rice-host cultivars (genotypes) depended significantly on a parasite population by host-genotype interaction. Genetic analysis using amplified fragment length polymorphism (AFLP) markers revealed that a small subset of AFLP markers showed 'outlier' genetic differentiation among sub-populations of S. hermonthica attached to different host cultivars. We suggest that, this indicates a genetic component to host range within populations of S. hermonthica, and that a detailed understanding of the genomic loci involved will be crucial in understanding hostparasite specificity and in breeding crop cultivars with broad spectrum resistance to S. hermonthica.

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“…To reduce the occurrence of homoplasy bins with fragment-length distributions that overlapped with adjacent bins were also removed. Raw peak intensity data output from Genotyper was subsequently transformed into a binary data matrix with AFLPScore R-script (Whitlock et al 2008). Given that our main objective was to investigate spatial genetic structure and it may arise both due to isolation-by-distance or due to spatial variation of selective forces affecting the distribution of alleles of specific loci (Beaumont and Balding 2004), only neutral loci were selected for the analyses.…”

Section: Dna Extraction and Aflp Genotypingmentioning

confidence: 99%

Rural avenues as dispersal corridors for the vulnerable saproxylic beetle Elater ferrugineus in a fragmented agricultural landscape

et al. 2015

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Understanding factors that limit gene flow through the landscape is crucial for conservation of organisms living in fragmented habitats. We analysed patterns of gene flow in Elater ferrugineus, an endangered click beetle living in old-growth, hollow trees in a network of rural avenues surrounded by inhospitable arable land. Using amplified fragment length polymorphism (AFLP) data, we aimed to evaluate if the landscape features important for the beetle's development are also important for its dispersal. By dividing the sampling area into 30 9 30 m cells, with each cell categorised into one of four classes according to its putative permeability for dispersing beetles, and by correlating matrices of genetic and landscape resistance distances, we evaluated which of the landscape models had the best fit with the observed kinship structure. Significant correlations between genetic and Euclidean distances were detected, which indicated that restricted dispersal is the main constraint driving differentiation between populations of E. ferrugineus. Out of 81 landscape models in total, 54 models yielded significantly weaker correlation between matrices of pairwise kinship and effective distances than the null model. Regression analysis pointed to avenues as having the highest and positive impact on the concordance between matrices of kinship and landscape distances, while open arable land had the opposite effect. Our study thus shows that tree avenues can function as efficient dispersal corridors for E. ferrugineus, highlighting the importance of saving such avenues to increase the connectivity among suitable habitat patches, thereby reducing the risk of local extinctions of E. ferrugineus as well as other saproxylic organisms.

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An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error

Cited by 61 publications

References 20 publications

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

Variation for host range within and among populations of the parasitic plant Striga hermonthica

Rural avenues as dispersal corridors for the vulnerable saproxylic beetle Elater ferrugineus in a fragmented agricultural landscape

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