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Open Access Research article

Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping

Tanja Strand12, Biao Wang1, Yvonne Meyer-Lucht1 and Jacob Höglund1*

Author Affiliations

1 Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden

2 Current address: Swedish Institute for Communicable Disease Control, Department of Analysis and Prevention, Nobels väg 18, Solna, SE-171 82, Sweden

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BMC Genetics 2013, 14:29  doi:10.1186/1471-2156-14-29

Published: 24 April 2013

Additional files

Additional file 1:

MHC primers and corresponding amplification lengths. The fragment column highlights the locus and region amplified with each primer pair. The PCR product length is given without primers.

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Open Data

Additional file 2:

Best evolutionary models estimated by Aikaike’s information criterion in jModelTest. The models were used to construct phylogenetic trees.

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Open Data

Additional file 3:

Alignment of black grouse MHC class II B exon 2 nucleotide sequences. Locus-designated sequences derived in the present study are indicated with 125 bp and 251 bp. Sequences indicated as BLB* are cloned in previous studies and not designated to locus, for example 202 bp cDNA sequences (from individual D870, see Table 1). Sequences likely to be from the same allele are grouped by grey shading.

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Open Data

Additional file 4:

Supplement for the test for positive selection. Likelihood values and parameter estimates for the different models calculated with CODEML implemented in PAML 4.6 [74]. M = model, lnL = Log-likelihood value. In the neutral model M0, ω is equivalent to averaged dN/dS. Dark grey shade highlights the significantly best models.

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Open Data

Additional file 5:

Neighbour Joining tree for exon 3. BLB1 and BLB2 sequences derived from black grouse (fosmid individual JHGO 213 [48] [GenBank JQ028669] and chicken [GenBank AB268588]. Goose [GenBank EU999169] was used as an outgroup.

Format: DOCX Size: 48KB Download file

Open Data