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Using model selection, we found six models with reasonable support (Δ i < 10) that explained the patterns in exam performance across the 23 classes (Table 1).
Diapriidae and Monomachidae are recovered in all analyses with reasonable support (V = 0.179), while Roproniidae and Pelecinidae are recovered in all analyses but with poor support (V = -0.234).
For two of the six loci, we find that the partition with strongest support is different from that assumed by Li et al. (2005), and for all six loci there are multiple partitions with reasonable support.
In this study, the donor and recipient lineages could be inferred in one putative eukaryote-to-eukaryote gene transfer event with reasonable support; ciliates were hypothesized to have acquired a gene from an Amoebozoa lineage.
Minor differences in the placement of some sequences are observed but the well-supported clades recovered by the Bayesian analysis are often present in the parsimony consensus trees with reasonable support (>75%).
This is a similar relationship to the results of Fukami et al. [ 12], although here we also show with reasonable support that Oulophyllia is monophyletic, and Caulastraea is an outgroup rather than nested within Oulophyllia (XVII-D).
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Consistent with this, H. parainfluenzae is known to have Hin-type USSs [ 15], and Christensen et al.'s rRNA and protein trees place P. pneumotropica close to P. multocida with reasonable bootstrap support; their rRNA tree also places H. aphrophilus and H. paraphrophilus close to H. influenzae with modest bootstrap support.
The concatenation and simultaneous analysis of 43 data partitions yielded a well resolved, single most parsimonious tree with reasonable bootstrap support.
Though growing evidence supports a relationship between cryptophytes and haptophytes [ 55, 56, 58], our extensive mitochondrial protein analyses did not reveal this relationship with reasonable bootstrap support, other than in a single protein gene tree (cob).
However, as in earlier phylogenetic analyses of eumetazoan AD domains [ 15], the AD domains from non-bilaterian ADAR1-like sequences were found to form a cluster with reasonable bootstrap support, suggesting that the ADAR1-like gene has undergone little diversification across evolutionary history.
Next, the raw transcriptome was filtered to discard poorly supported transcripts, and to maintain transcripts with strong evidence of protein coding regions and reasonable support for expression.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com