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Additionally, we examine the relationship between antagonism and relative genetic difference between pairs of strains inferred from patterns of DNA sequence divergence analyses.
Downstream population divergence analyses utilized unphased genotype data.
All nucleotide sequence divergence analyses were conducted using the Maximum Composite Likelihood method in MEGA 4.0.2.
dN/dS ratios for all four species used in the divergence analyses.
The alignment and the neighborjoining tree were used as input for the functional divergence analyses.
Two divergence analyses were selected and presented here to show the maximum range of estimated dates.
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Phylogenetic relationships and nucleotide divergence analyse (intra and inter genotype) were established with MEGA4 [31] using the Kimura 2-parameter correction in which the transition/transversion ratio was estimated from the data [32].
Divergence dating analyses can be sensitive with regard to incorrectly placed fossil calibrations [ 58– 60], but our analyses, sampling from the prior, show no indication of detrimental interactions between calibration priors.
The constraints above were used in all divergence time analyses.
We thank J. Esselstyn, C. Linkem, J. Oaks, and J. Sukumaran for stimulating discussion regarding Southeast Asian biogeography and divergence time analyses.
The results of the divergence time analyses presented herein indicate that the first pigmented stramenopiles most likely evolved between the mid-Neoproterozoic and the Early Devonian.
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