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Since legumes comprise a diverse clade separated by a long branch length from other groups, they can strongly influence patterns of phylogenetic dispersion of plots where they colonize.
However, because acoelomorphs evolve at a very high rate (except perhaps for myosin II), their basal emergence can be easily explained by a long branch attraction (LBA) [10] artefact triggered by the distantly related outgroup (Cnidaria).
Results showed that human and gar genomes clustered together separated from the two teleost genomes by a long branch.
The discrepancy between the two datasets does not seem to be explainable by a long branch attraction artefact.
Then it could happen that one or more sequences in the subtree are connected accidently to the rest by a long branch attraction.
Group II.A is strongly supported, with 100% bootstrap support and is separated by a long branch from other cluster II PA.
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A second subclade within clade C (group C2), is separated by a long branch-length and also has robust bootstrap support.
A related method consists in 'breaking' a long branch, by adding a series of intermediate taxa thought to emerge along this branch [ 16].
However, in both these trees, one subclade of Prochlorococcus strains, which is referred to as the low B/A ecotype subgroup [ 40, 41], was separated from all others Prochlorococcus strains by a long-branch.
MIT9515, CCMP1986, MIT9312, MIT9215, MIT9301 and AS9601) formed a distinct subclade that was well separated from all other Clade C species/strains by a long-branch and 100% bootstrap score (Fig. 1 and additional file 2)[ 23, 41].
With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment.
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