Open Access Highly Accessed Research article

African signatures of recent positive selection in human FOXI1

Andrés Moreno-Estrada13, Estel Aparicio-Prat1, Martin Sikora1, Johannes Engelken1, Anna Ramírez-Soriano1, Francesc Calafell12 and Elena Bosch12*

Author Affiliations

1 Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, C/Dr. Aiguader 88, 08003 Barcelona, Spain

2 Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain

3 Department of Genetics, Stanford University School of Medicine, USA

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BMC Evolutionary Biology 2010, 10:267  doi:10.1186/1471-2148-10-267

Published: 1 September 2010

Additional files

Additional file 1:

Table S1: Coriell repository numbers.

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Additional file 2:

Table S2: Amplification and sequencing primers.

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Additional file 3:

Figure S1: Phylogeny of the five mammalian species used in PAML analysis. Each branch is labeled with the corresponding estimate of ω calculated under a free branch model [44] with the codeml program within PAML using standard parameters [28]. Inferred synonymous and non-synonymous substitutions are indicated within brackets.

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Additional file 4:

Figure S2: Alignment of the five FOXI1 mammalian sequences used in PAML analysis.

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Additional file 5:

Table S3: Significance of the likelihood ratio tests of positive selection performed on the human lineage for the FOXI1 gene.

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Additional file 6:

Figure S3: Median Joining Network of human FOXI1 haplotypes. Nodes in the median joining network are proportional to frequencies and branch lengths to the number of polymorphic base substitutions.

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Additional file 7:

Figure S4: Distribution of low-frequency minor alleles. The proportion of SNPs with a minor allele frequency (MAF) of less than 0.10 within 100 kb sliding windows is plotted for each population. Solid dots represent values above the 95th percentile for each population, whereas open dots are values below the 95th percentile.

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Additional file 8:

Figure S5: Distribution of high-frequency derived alleles. The proportion of SNPs with a derived allele frequency (DAF) greater than 0.80 within 100 kb sliding windows is plotted for each population. Solid dots represent values above the 95th percentile for each population, whereas open dots are values below the 95th percentile.

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Additional file 9:

Figure S6: Pattern of linkage disequilibrium around FOXI1 in the Yoruba population from the CEPH-HGDP diversity panel. Linkage disequilibrium from position 169,401,507 to 169,544,856 on chromosome 5, NCBI build 36.3. Green boxes represent significant core haplotypes from the LRH test and are labelled with letters d-h as in Table 4.

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Additional file 10:

Table S4: Functional characterization and allele frequencies for functionally relevant SNPs within ~ 140 kb containing the FOXI1 gene.

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