Estimating levels of inbreeding using AFLP markers

Dasmahapatra, Kanchon K.; Lacy, Robert C.; Amos, William

doi:10.1038/sj.hdy.6801075

Cited by 45 publications

(41 citation statements)

References 70 publications

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“…However, even highly accurate F i estimates may poorly reflect the population average if the number of individuals is small. Our method (F B ) provides somewhat better estimates of the average inbreeding as compared with the method proposed by Dasmahapatra et al (2007) (F FM ). The two methods differ fundamentally, because, whereas the F B estimator is well founded in the Bayesian statistical methodology, F FM is rather a heuristic approach, in which the Method-ofMoments estimator is adjusted based on the specific assumptions.…”

Section: Methodological Considerationsmentioning

confidence: 88%

“…The main benefit of this Abbreviation: RMSE, root mean square error. N, sample size; L, number of loci; F FM , the frequency-matching estimator (Dasmahapatra et al, 2007); F B , the Bayesian estimator (developed in this study). The results are based on 50 repetitions for each scenario.…”

Section: Discussionmentioning

confidence: 99%

“…Once phenotypes were generated they were stored as input files for estimating the inbreeding coefficient using two different applications: the FAFLPcalc Excel macro implementing the method of Dasmahapatra et al (2007) (available at http://www.ucl.ac.uk/taxome/kanchon/ #publications) and I4A, a stand-alone Windows programme implementing the Bayesian approach introduced in this paper. In the case of I4A we used the prior values of beta-distributions equal to a ¼ b ¼ a p ¼ b p ¼ 1.0 (corresponding to an 'uninformative' flat distribution) and 60 000 repetitions, including a 10 000-step burn-in.…”

Section: For Eachmentioning

confidence: 99%

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Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

2011

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Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50-100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.

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Section: Methodological Considerationsmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: For Eachmentioning

confidence: 99%

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Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

2011

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“…The AFLP protocol was similar to that used in Vos et al (1995) and Dasmahapatra et al (2008). Briefly, 100-400 ng of genomic DNA was first digested using TaqI (5 U in a 10 ml volume, 65 1C for 2 h) and then with EcoRI (5 U in a 20 ml volume, 37 1C for 2 h).…”

Section: Methodsmentioning

confidence: 99%

Pinniped phylogenetic relationships inferred using AFLP markers

2009

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Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic reconstruction in plants but their use in animal taxa has been limited, and in mammals rare. In addition, their use has been largely limited to shallow relationships amongst species or subspecies. Here, we genotype 23 pinniped species for 310 AFLP markers and find a strong phylogenetic signal, with individuals coclustering within species, and overall a good agreement between our phylogeny and those constructed using mitochondrial DNA and nuclear sequences even at nodes B15 million years old. Although supporting the existing ideas about pinniped relationships, our data shed light on relationships within the hitherto relatively unresolved Phocine species group, and provide further supporting evidence for raising two subspecies of Zalophus californianus, Z. c. californianus and Z. c. wollebaeki, to species level. Plotting AFLP divergence time estimates against those based on both mtDNA and nuclear sequences we find strong linear relationships, suggesting that the different markers are evolving in a clocklike fashion. These data further emphasize the utility of AFLP markers as general tools for phylogenetic reconstruction.

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“…Most marker-based inbreeding estimators are developed for estimating the average F of individuals, or population level inbreeding (for example, Li and Horvitz, 1953;Robertson and Hill, 1984;Hill et al, 1995;Ayres and Balding, 1998). A few estimators are proposed to use unlinked codominant markers (Ritland, 1996;Ritland and Travis, 2004;Carothers et al, 2006;Wang, 2007), unlinked dominant markers (Dasmahapatra et al, 2008) or linked genomic markers (Leutenegger et al, 2003) to estimate individual inbreeding coefficients. Some of the estimators were compared with MLH in estimating individual inbreeding coefficients using empirical and simulated genomic marker data (Polašek et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

A new likelihood estimator and its comparison with moment estimators of individual genome-wide diversity

Wang

2011

Heredity

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The inbreeding coefficient of an individual, F, is one of the central parameters in population genetics theory. It has found important applications in evolutionary biology, conservation and ecology, such as the study of inbreeding depression. In the absence of detailed and reliable pedigree records, researchers have developed quite a few estimators to estimate F or the genome-wide homozygosity from genetic marker data. The statistical properties and comparative performances of these metrics are rarely known, however, which impedes an informed choice of the most appropriate one in practical applications. In this investigation, I propose a new likelihood F estimator that makes efficient use of marker information and takes into account of allelic dropouts, null alleles and prior knowledge of inbreeding. I compare the likelihood estimator with three moment estimators of F and three metrics of genomic homozygosity (or heterozygosity) by analysing both simulated and empirical datasets. It is shown that the likelihood estimator invariably outperforms the other estimators and metrics across all datasets analysed. For a typical dataset in heterozygosity-fitness correlation studies involving 10-20 microsatellites and 50 individuals, the correlation between the likelihood estimator and F (the simulated true inbreeding coefficient) is about 8B35% higher than that between the moment estimators and F. A frequently applied metric, multilocus heterozygosity (MLH), and an F estimator based on the consideration of the proportion of alleles in homozygous conditions, F R , are shown to have particularly poor performances. The low correlation between MLH and fitness traits, which is widely observed in numerous empirical studies, might be partially caused by the adoption of this inefficient estimator of genomic inbreeding.

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Estimating levels of inbreeding using AFLP markers

Cited by 45 publications

References 70 publications

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Pinniped phylogenetic relationships inferred using AFLP markers

A new likelihood estimator and its comparison with moment estimators of individual genome-wide diversity

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