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Spruce can grow at an extra low temperature (LT), and is inferred with important antifreezing gene resources.
A decreasing trend is inferred with increase in temperature.
Cloud-top pressure is inferred with uncertainty lower than 10%% when COT is larger than 0.3.
Then, the phylogenetic tree obtained from the nucleotide aligniment is imported in MacClade and the putative origin of each ancestral sequence (i.e. internal node) in the tree is inferred with the Fitch algorithm [79] by finding the most parsimonious reconstruction (MPR) of the ancestral character (this can be accomplished by selecting the Trace character option in the Trace menu of MacClade).
The putative origin of each internal sequence (i.e. internal node) in the tree is inferred with the Fitch algorithm.
See also Figure 3 figure supplement 1 for a description of how these statistics vary when the HMM is inferred with 4 14 states.
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Phylogenetic relationships among species were inferred with PhyML (PHYlogenetic inferences using Maximum Likelihood) [ 44] using the WAG model.
Gene ages were inferred with previously described methods77.
Phylogenetic trees of the individual segments were inferred with the maximum likelihood (ML) method implemented in IQ-TREE package 0.9.6 24.
ML phylogenetic trees were inferred with the PhyML program29, using the best-fit model of nucleotide substitution selected using the jModelTest program30.
The adults used in crosses 10, 11, 12 and 13 were derived from offspring of cross 9, so the shell genotype could be inferred with extra confidence.
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