Open Access Research

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Laurent AF Frantz1*, Joshua G Schraiber2, Ole Madsen1, Hendrik-Jan Megens1, Mirte Bosse1, Yogesh Paudel1, Gono Semiadi3, Erik Meijaard45, Ning Li6, Richard PMA Crooijmans1, Alan L Archibald7, Montgomery Slatkin2, Lawrence B Schook8, Greger Larson9 and Martien AM Groenen1

Author Affiliations

1 Animal Breeding and Genomics Group, Wageningen University, De Elst 1, Wageningen, WD 6708, The Netherlands

2 Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA

3 Puslit Biologi LIPI, Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Jawa Barat, Indonesia

4 People and Nature Consulting International, Vila Lumbung House no. 6, Jl. Kerobokan Raya 1000x, Badung 80361, Bali, Indonesia

5 School of Archaeology and Anthropology, Australian National University, Canberra ACT 0200, Australia

6 State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, PR China

7 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK

8 Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois 61801, USA

9 Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK

For all author emails, please log on.

Genome Biology 2013, 14:R107  doi:10.1186/gb-2013-14-9-r107

Published: 26 September 2013

Additional files

Additional file 1:

Tables S1 to S4, with information on sequence data and alignment results.

Format: PDF Size: 104KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Figure S1, a species cladogram with support from various analyses.

Format: PDF Size: 102KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Table S5, containing results from clade relative frequency analysis.

Format: PDF Size: 59KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Text with additional results and discussion for admixture analysis.

Format: PDF Size: 323KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Table S8, which contains the full results from the D-statistics analysis.

Format: PDF Size: 76KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Text that contains information about fossil calibration.

Format: PDF Size: 98KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Figure S3 describing the demographic history of the population from MSEA.

Format: PDF Size: 275KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Figure S4, a phylogenetic tree constructed using SNPs sequenced with the Illumina Porcine SNP60 array.

Format: PDF Size: 191KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data