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Open Access Research article

Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

Ryan C Garrick12*, Paul Sunnucks3 and Rodney J Dyer1

Author Affiliations

1 Department of Biology, Virginia Commonwealth University, Richmond, Virginia 23284, USA

2 Current Address: Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA

3 Australian Centre for Biodiversity, School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia

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BMC Evolutionary Biology 2010, 10:118  doi:10.1186/1471-2148-10-118

Published: 30 April 2010

Additional files

Additional file 1:

Increase over time in the use of PHASE in empirical studies relating to phylogeography, speciation or hybridization. Figure is based on the 60 articles included in our literature survey (see Table 1 in the main text). All of these studies focus on non-primate animals and used PHASE to reconstruct haplotypes from directly sequenced non-coding nuclear loci.

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Additional file 2:

Frequency distribution of the relationship between number of segregating sites (S) and number of different alleles (AN) in the 500 simulated datasets from which 35 (solid circles) were arbitrarily selected for further analysis using PHASE. Figure shows that none of the 35 datasets are atypical (i.e., outliers), and so the results presented in the main text are free from bias relating to the dataset selection procedure.

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Additional file 3:

Correlation coefficients between the four measures of dataset polymorphism. In this figure, values were calculated from the pooled empirical datasets (above diagonal), and pooled simulated datasets (below diagonal). S, number of segregating sites; AN, number of different alleles; GN, number of different genotypes; HO, observed heterozygosity.

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Additional file 4:

Supplementary references. List of 60 papers from 18 journals included in the literature survey of empirical studies that used PHASE for haplotype reconstruction (see Table 1 of the main text).

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Additional file 5:

Relationship between alternative measures of dataset polymorphism (x-axis) and the number of unresolved genotypes (y-axis). Simulated and empirical datasets are represented by solid circles and open circles, respectively. A-B, number of segregating sites (S) under the 0.90 and 0.60 thresholds; C-D, number of different alleles (AN) under the 0.90 and 0.60 thresholds; E-F, number of different genotypes (GN) under the 0.90 and 0.60 thresholds; G-H, observed heterozygosity (HO) under the 0.90 and 0.60 thresholds. All regressions were significantly positive (P < 0.05) for simulated data, but not for the empirical data.

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