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It remains an open issue why these four phylogenetic methods suggest a different basal node for the genus based on mtDNA and nuclear data sets.
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Ancient haplotypes are named according to the letter of their haplogroup supplemented by a number or a number and a letter depending on how far they are from the basal node (for example: haplotype D3 is separated from D by 1 mutation, and haplotype D3a by 2 mutations).
Standard procedures for fossil calibrations [20] use the basal node of the crown group for the calibration (i.e., the fossil age is placed at the immediate ancestor to the extant lineage).
Moreover, the mtDNA genealogy illustrates concepts such as the MRCA (Most Recent Common Ancestor) both in terms of the ultimate basal node of the tree and for individual clades, such as that comprising the out-of-Africa component of human history.
Our maximum credibility phylogenetic tree shows strong support for the monophyly of the clownfishes with a high posterior probability (PP = 0.98) for the basal node of the clade.
We used the only fossil calibration point available for the basal node of the Pomacentridae to obtain absolute divergence time estimates.
To summarize gene expression across species, we used the estimated expression levels for the most basal node of the tree.
Lastly, an outgroup to all Hymenoptera was required in order to test for a significant difference in species richness at the basal node of the tree.
The mean difference of all pairs of sequences linked through the basal node of the M strain cluster was 0.028+/−0.004 nucleotide substitutions/site (ns/s), but only 0.009+/−0.002 ns/s for the D strain.
The basal node of the 16 South American cCP sequences linked sequences that differed by a mean of 0.1397+/−0.024 ns/s.
Our AFLP tree obtained better resolution with over 1000 multilocus AFLP characters, although some basal nodes for Perissodus species were still not well resolved.
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