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Analysis of multiple gene phylogenies provides further evidence for outcrossing.
In addition, single gene phylogenies are much more error-prone than multiple gene phylogenies.
Finally, an approach using multiple gene phylogenies has firmly established that most host races of M. violaceum represent multiple independent evolutionary lineages, highly specialized on a single or a few host species [ 29].
Nevertheless, multiple gene phylogenies support several robust groupings of excavates, of which three are relevant here: (1) diplomonads plus parabasalids (and other taxa collectively known as Metamonada); (2) Trimastix and oxymonads (Preaxostyla); and (3) Euglenoids and kinetoplastids (Euglenozoa) [ 30].
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We inferred a multiple gene phylogeny of anther smut strains from 21 host plants from several geographic origins, complementing a previous study on the delimitation of fungal species and their host specificities.
Cryptophyta, Katablepharidae, and Haptophyta formed a clade with moderate to strong support, which is consistent with recent multiple-gene phylogenies that suggested a close relationship between Cryptophyta and Haptophyta (Katablepharidae was not examined in these studies) [55], [56].
A multiple-gene phylogeny inferred from these data shed light on the evolutionary relationships within the grass family.
The contrast of multiple independent gene phylogenies is thus another key in testing taxonomic hypotheses.
Finally, the multiple plastid gene phylogenies also provide strong support for the monophyly of the euasterid II clade (Figs. 2, 3).
In this study, we present a new algorithm for the inference of explicit weighted consensus networks from a collection of trees (e.g., multiple single-gene phylogenies), with or without prior knowledge of the species phylogeny.
Different rates of evolution, multiple gene duplications and convergent evolution, as a consequence of specific adaptation to environmental demands, may be the reason for inconsistencies seen in comparisons of phylogenies deduced from trp genes or rRNA [ 16].
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