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Our analyses suggest that multiple independent losses of photosynthesis have occurred in the non-photosynthetic trebouxiophytes, which have convergently lost a similar set of genes related to photosynthesis in the plastid and nuclear genomes.
A less likely explanation is multiple independent losses of the operon from all other Firmicutes lineages.
As already mentioned, this loss of helicase genes, if confirmed when more information for these groups is available, would mirror the multiple independent losses of those same genes in animal lineages [11].
As the alternative explanation (its presence at the root of all eukaryotes combined with multiple, independent losses in various eukaryotic lineages) is less parsimonious, we tend to think HGT is the most likely explanation of the observed results.
Within the Plakinastrella-like genomes, one or two introns are present in cox1 of Plakinastrella sp., Plakina crypta and Plakina trilopha but absent elsewhere, an observation we interpret as multiple independent losses [86].
Thus, no multiple independent losses were counted (see Fig. 1c).
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The presence of an extra trnM within the latter two lineages could represent a character state that was (1) independently derived multiple times, (2) derived once with multiple independent secondary losses or (3) both derived and lost multiple times independently.
When coupled to a strategy of phyletic pattern analysis, the approach allows differentiation of species-specific gene loss from multiple independent gene loss.
This scenario is, however, unlikely since multiple independent character losses were required.
However, this assumption would require multiple independent gene losses in diverse invertebrate lineages.
Multiple, independent gene losses in angiosperms have been demonstrated for other genes including infA [ 50], rps16 [ 48] and accD [ 51, 52].
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multiple independent spikes
multiple independent annotators
multiple independent reports
multiple independent confirmations
multiple independent tests
multiple independent channels
multiple independent sources
multiple independent entities
multiple independent datasets
multiple parallel losses
multiple independent estimates
multiple independent hybrids
multiple allelic losses
multiple independent axes
multiple independent experts
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