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These methods, however, rely on an initial motif discovery phase using generic pattern-finding TEIRESIAS software [9], which returns all shared patterns regardless of evolutionary relationships and with only crude length and complexity control.
Regardless of evolutionary origins, the observation that Fov strains in cultivated field soils were overwhelmingly outnumbered by nonpathogenic (on cotton) lineage E isolates was surprising for two reasons.
Phenetics seeks to classify organisms based on observable differences regardless of evolutionary history, while cladistics, which also examines observable characteristics, has the explicit goal of inferring shared ancestry and constructing a hierarchical classification.
This observation can be rationalized within the current formulation of the sequence homology concept [ 1- 6]: SP/TM regions are essentially hydrophobic stretches that, in a first approximation, are similar to each other regardless of evolutionary origin due to functional pressures.
Two mutations, which are apparently specific for strains circulating in Reunion and Mayotte, consist of A1028→V and D1086→E substitutions with reference to all other CHIKV strains characterized to date, regardless of evolutionary lineage (amino acid positions refer to the sequence of the original Ross isolate, accession no. AF490259).
We regret that our manuscript was unclear on an important point: our goal was to evaluate — regardless of evolutionary age — whether any of the novel readthrough events we identified occur because they are biologically important or, alternatively, simply because they can occur without incurring a significant fitness disadvantage (i.e., are selectively neutral or nearly neutral).
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The most-direct difference between the two methods is that phenetics classifies species by using as many characteristics as possible and arranges them by similarity regardless of any evolutionary relationships.
Regardless of the evolutionary history of the PDR5 gene and the mechanism for the AmB-sensitivity change in YJM789, our experimental results might imply a new drug-resistance strategy in pathogenic yeasts, i.e., sacrificing an important function in one drug condition for a minor fitness gain in other drug conditions.
Therefore, a sufficiently large k will overcome homoplasy, regardless of the evolutionary distance between species.
Regardless of their evolutionary history, haplotypes 1 and 2 provided an entrée to the genetics of morphological variation of ray pattern in C. briggsae.
Regardless of the evolutionary origin of the regulatory substrate, our results still explain a non-adaptive increase in regulatory complexity through mutation and genetic drift.
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