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While there has been some success in identifying important subfamilies in metagenomics data [3] [6], there are also immense challenges ahead as tools and computational infrastructure often do not scale with the increase in metagenomics data and as many protein families have complicated evolutionary histories.
The analysis presented here highlights the functional diversity and complicated evolutionary relationships of M13 peptidases.
The latter 76 families were not analyzed further (due to their overly complicated evolutionary histories).
The copy number variation on the phylogenetic tree reflected complicated evolutionary patterns of actin gene family.
As a result, the reconstructed trees and networks are much simpler than the true phylogeny, distorting the originally complicated evolutionary histories.
New and complicated evolutionary models based only on gene tree conflicts should not be advanced without explicit experimental attempts to falsify them.
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Considerable localized differentiation in evolutionary rates has not previously been observed in FMDV, and although potentially informative concerning epidemiology and evolution, it also complicates evolutionary estimates based on global or widespread sample collections.
Such a result demonstrates a strong advantages in phenotype discrimination over the previous work [ 17, 23, 24], just as we pointed out before, which employed quite complicate evolutionary algorithm (PSO-SVM) to collect a set of informative peaks and achieved 90%+ diagnosis accuracy under a 5-fold cross validation [ 23].
The radical alterations to archipelago's geography caused by this cyclical coalescence and isolation of islands is likely to have complicated the evolutionary history of several iconic Galapagos species, notably the land iguanas, lava lizards, leaf-toed geckos and racer snakes.
Together, these data indicate that X. bovienii tccC genes have complicated recent evolutionary histories and that their functions likely vary among X.
Complicating the evolutionary history of viruses is the evidence that many of the most complex types evolved by acquiring and exchanging genes with their hosts as they evolved [2].
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