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The remaining three lineages; however, are morphologically homogeneous and may represent cryptic species.
The remaining three lineages, all purportedly containing some species that harbor plasmids, have elevated levels of most of these gene groups compared to TG rickettsiae.
The remaining three lineages, L, S and P, are not predicted to bind peptides and are lost in some species.
This latter value was smaller in all resampling replications pointing to a younger age of the modern haplochromines compared to the remaining three lineages of haplochromines sensu lato.
The remaining three lineages comprised samples from geographically proximate countries (Sri Lanka and the sample from Madras, India Thailand and Laoss; and Pakistan, India, and Nepal).
A data mining procedure from the jatropha genomic sequence using the BLAST algorithm from RT sequences of other copia-type families in other plant species, including those of the remaining three lineages (Maximus, Ivana, and Bianca), detected jatropha RT sequences that were not isolated using degenerate primers (data not shown).
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The remaining two lineages occur naturally only north of the current study area and so their presence is not expected.
Of the remaining eight lineages that infected multiple hosts, four belonged to each of the Plasmodium and Haemoproteus groups, respectively (Table S2).
The likelihood test was performed as a one-sided chi-square test of the null hypothesis H0 assuming one d N / d S ratio among all three lineages versus alternative hypotheses HA and HB allowing for two d N / d S ratios – one for wBm or wMel respectively, and a second for the remaining two lineages (branch-specific model).
Excluding all five taxa resulted in a fully resolved, well-supported UCE phylogeny for the remaining six formicine lineages (Fig. 2c).
DOI: http://dx.doi.org/10.7554/eLife.02949.011 The remaining two experimental lineages (L2E and L4E) lost detectable SDS-stable Sup35 NM aggregates at R3 and R4, respectively.
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