Open Access Research article

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals

João Paulo Machado12, Warren E Johnson3, Stephen J O'Brien3, Vítor Vasconcelos14 and Agostinho Antunes134*

Author Affiliations

1 CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal

2 Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Portugal

3 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA

4 Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal

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BMC Evolutionary Biology 2011, 11:342  doi:10.1186/1471-2148-11-342

Published: 21 November 2011

Additional files

Additional file 1:

Table S1. List of species used for the evolutionary genomic analyses.

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Additional file 2:

Table S2. Tree topology and phylogenetic signal tests.

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Additional file 3:

Figure S1. Conserved Non Coding Sequences in the 26 mammalians.

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Additional file 4:

Figure S2. Alignment of Homo sapiens sequence with the three birds in the present study.

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Additional file 5:

Table S3. Positive selection in branch-site model using rodents as foreground branch.

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Additional file 6:

Table S4. The sites showing positive selection at codon level.

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Additional file 7:

Table S5. The sites showing positive selection in TreeSAAP.

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Additional file 8:

Table S6. The sites showing positive selection in CONTEST.

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Additional file 9:

Table S7. Amino acids showing directional evolution in MEPE.

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Additional file 10:

Table S8. MEPE protein sites showing directional evolution.

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Additional file 11:

Figure S3. "Disordered" regions in human sequence identified using PrDOS.

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Additional file 12:

Figure S4. Alignment of MEPE showing the functional motif and the amino acids under positive selection.

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