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Fig. 4 | BMC Evolutionary Biology

Fig. 4

From: Positive selection in octopus haemocyanin indicates functional links to temperature adaptation

Fig. 4

a) Protein sequence conservation estimated using the Jensen-Shannon divergence [30], which identifies conserved sites as deviations of a probability distribution from the overall amino acid distribution of the respective BLOSUM62 alignment as background and also accounts for conservation in neighbouring sites. Greater scores indicate higher sequence conservation. b) Estimated differences between nonsynonymous and synonymous substitutions (dN-dS) at each site of the haemocyanin nucleotide sequence inferred from Single Likelihood Ancestral Counting (SLAC) normalised to the total length of the underlying maximum likelihood tree. c) Natural selection in octopus haemocyanin. The y-axis indicates the cumulative number of selection tests that yielded significant results for positive or negative selection at an individual site. Positively selected sites confirmed by two or more tests were marked red. All analysis was performed for two separate alignments, containing 113 or 126 sequences respectively, and covering in total a 396 amino acid long coding region of the haemocyanin’s functional units f and g. Residue positions refer to the published full haemocyanin sequence of Enteroctopus dofleini [UniProt: O61363] [23, 24]. Significance thresholds were: p-values ≤ 0.10 for SLAC, ≤ 0.10 for FEL, MEME and PRIME; Posterior Probability ≥ 0.90 for FUBAR; Bayes Factor ≥ 0.50 for EF.

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