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Open Access Highly Accessed Research article

On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

Margarida Coelho12, Fernando Sequeira3, Donata Luiselli4, Sandra Beleza1 and Jorge Rocha12*

Author Affiliations

1 IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, R Dr Roberto Frias s/n, 4200-465 Porto, Portugal

2 Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal

3 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal

4 Dipartimento di Biologia Evoluzionistica Sperimentale, Universita di Bologna, Via Selmi, 3 Bologna, Italy

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BMC Evolutionary Biology 2009, 9:80  doi:10.1186/1471-2148-9-80

Published: 21 April 2009

Additional files

Additional File 1:

MtDNA sequence data from southwestern Angola. The table displays HVS-I and HVS-II sequence data and haplogroup classifications in population groups sampled in the Namibe province.

Format: XLS Size: 74KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional File 2:

NRY haplotype data from southwestern Angola. The table displays NRY haplotypes defined by UEP and STRs in population groups sampled in the Namibe province.

Format: XLS Size: 54KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 3:

Typing procedure for lactase persistence mutations. The file provides details on the genotyping method for the following polymorphisms associated with lactase persistence: G/C -14010; T/G -13915; C/T -13910 and C/G -13907.

Format: PDF Size: 19KB Download file

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Additional File 4:

MtDNA comparative African data. The table summarizes previously published mtDNA HVS-I datasets on African populations, here considered for comparative purposes.

Format: PDF Size: 49KB Download file

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Additional File 5:

NRY comparative African data. The table summarizes previously published NRY datasets on African populations, here considered for comparative purposes.

Format: PDF Size: 45KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 6:

The IM framework and the splitting of the western and eastern streams of Bantu migrations. The scheme presents the basic parameters of the IM model in the context of the Bantu expansion. NA = population effective size of the ancestral population; N1 = current population size in the Southwest edge; N2 = current population size in the Southeast edge; m1 = migration rate from the eastern into the western stream; m2 = migration rate from the western into the eastern stream. Note that the migration parameters are identified by the destination of migrants as time goes forward.

Format: PDF Size: 6KB Download file

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Open Data

Additional File 7:

Patterns of mtDNA lineage sharing by haplogroup. The figure shows the fractions of lineage sharing between southwestern Angola and other African regions for the most common mtDNA haplogroups (see Figure 3).

Format: PDF Size: 13KB Download file

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Open Data

Additional File 8:

Median-joining network derived from African HVS-I mtDNA sequences belonging to haplogroup L0d. The figure shows the phylogenetic relationships between the mtDNA L0d sequences from southwestern Angola and from other African populations. Each circle represents a different haplotype. The area of the circles is proportional to the frequency of the haplotype in the populations. The branch lengths are proportional to the number of mutations separating two sequences.

Format: PDF Size: 11KB Download file

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Additional File 9:

Median-joining network derived from African Y-chromosome STR-haplotypes belonging to haplogroup B2b. The figure shows the phylogenetic relationships between Y-chromosome B2b haplotypes from southwestern Angola and from other African populations. Haplotypes were defined with a common set of 5 STR loci: DYS19, DYS389I, DYS389II, DYS390, and DYS392. The area of the circles is proportional to the frequency of the haplotype in the populations. The branch lengths are proportional to the number of mutations separating two haplotypes.

Format: PDF Size: 63KB Download file

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Open Data

Additional File 10:

Probability densities for the basic demographic parameters of the IM model. The figure provides marginal posterior probability densities for independent runs of the program IMa using the Y-chromosome STR haplotype dataset (L = likelihood).

Format: PDF Size: 77KB Download file

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Open Data

Additional File 11:

Probability densities for the basic demographic parameters of the IM model. The figure provides marginal posterior probability densities for independent runs of the program IMa using the mtDNA HVS-I sequence dataset (L = likelihood).

Format: PDF Size: 73KB Download file

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Open Data

Additional File 12:

Probability densities for the basic demographic parameters of the IM model. The figure provides marginal posterior probability densities for independent runs of the program IMa using the joint mtDNA and Y-chromosome datasets (L = likelihood).

Format: PDF Size: 32KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data