Abstract
Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.
Highlights
Accepted: 25 January 2021The word homoplasy was used for the first time by the British zoologist Lankester in 1870 to dissect the general world “homology” in “homogeny” and “homoplasy,” using the following definition: “homoplasy includes all cases of close resemblance of form which are not traceable to homogeny” [1]
There is still no quantification of this phenomenon in microorganisms in which the homoplasy can be due to horizontal gene transfer and there is no quantification for rRNA markers widely used in taxonomy and phylogeny [26,28]
We took into consideration different taxonomic models and analyzed them with HomoDist using the rRNA markers ITS and LSU, reporting the consistency index (CI), that is the complement to 1 of homoplasy index (HI), since CI is a direct measure of the tree quality
Summary
The word homoplasy was used for the first time by the British zoologist Lankester in 1870 to dissect the general world “homology” in “homogeny” and “homoplasy,” using the following definition: “homoplasy includes all cases of close resemblance of form which are not traceable to homogeny” [1]. Whilst the term homogeny has turned to be homology in current biological semantics, the term homoplasy survived and was taken over by Willy. Current phylogenetics refer to homoplasy as the situation in which traits are common to taxa not sharing a common ancestry, that can be caused by convergent evolution, reversal to ancestral trait and horizontal gene transfer (HGT) [3,4]. The need of homoplasy quantification as an a posteriori control comes directly from the first The first aspect relates to the fact that homoplasy is the phylogenetic noise hampering the search of a consistent tree [7] and influencing clade support metrics as the bootstrap [7], homoplastic sites introduce more information on the phylogenetic structure under study [8].
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