The role of laterally transferred genes in adaptive evolution

Additional File 9:

Curvature of likelihood change in different models.

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Additional File 14:

The likelihood value shows a continuous pattern of change as the insertion/deletion rate changes in the reversible gain/loss model.

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Additional File 15:

The likelihood surface with different rates of insertion/deletion on external/internal branches in the reversible gain/loss model.

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Additional File 10:

Non-synonymous change of the genes present in Cgl and Cef. A, genes present in Cgl and Cef; B, genes present in Cgl and Cef and having matches in the database. Genes show similar rates of evolution by only looking at the genes having matches elsewhere the genome database.

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Additional File 11:

Synonymous change of the genes present in Cgl and Cef. A, genes present in Cgl and Cef; B, genes present in Cgl and Cef and having matches in the database. Genes show similar rates of evolution by only looking at the genes having matches elsewhere the genome database.

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Additional File 12:

K_a/K_s ratio of the genes present in Cgl and Cef. A, genes present in Cgl and Cef; B, genes present in Cgl and Cef and having matches in the database. Genes show similar rates of evolution by only looking at the genes having matches elsewhere the genome database.

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Additional File 1:

The phyletic patterns of the Corynebacterium taxa. (cut-off: expect value less than 10^-20 and match length over 85%)

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Additional File 2:

The phyletic patterns of the Corynebacterium taxa (cut-off: expect value less than 10^-10 and match length over 70%)

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Additional File 3:

The phyletic patterns of the Corynebacterium taxa (cut-off: expect value less than 10^-05 and match length over 50%)

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Additional File 4:

Insertion/deletion rates inferred from the maximum likelihood analysis assuming different rates for external and internal branches (cut-off: expect value less than 10^-10 and > 70% match length)

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Additional File 5:

Insertion/deletion rates inferred from the maximum likelihood analysis assuming different rates on each branch of the phylogeny (cut-off: expect value less than 10^-10 and > 70% match length)

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Additional File 6:

Insertion/deletion rates inferred from the maximum likelihood analysis assuming different rates for external and internal branches (cut-off: expect value less than 10^-05 and > 50% match length)

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Additional File 7:

Insertion/deletion rates inferred from the maximum likelihood analysis assuming different rates on each branch of the phylogeny (cut-off: expect value less than 10^-05 and > 50% match length)

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Additional File 13:

An alternative topology of the concatenated genes. The insertion/deletion rates on external branches and internal branches were studied.

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Additional File 8:

Insertion/deletion rates inferred from the maximum likelihood analysis assuming different rates for external and internal branches. Likelihood was estimated using the alternative topology and a cutoff with expect value less than 10^-20 and > 85% match length.

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Additional File 16:

Decreased GC content of recently acquired genes.

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