Brief. Bioinformatics - The impact of HGT on phylogenomic reconstruction methods.

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Resumo

Supermatrix and supertree analyses are frequently used to more accurately recover vertical evolutionary history but debate still exists over which method provides greater reliability. Traditional methods that resolve relationships among organisms from single genes are often unreliable because of the frequent lack of strong phylogenetic signal and the presence of systematic artifacts. Methods developed to reconstruct organismal history from multiple genes can be divided into supermatrix and supertree approaches. A supermatrix analysis consists of the concatenation of multiple genes into a single, possibly partitioned alignment, from which phylogenies are reconstructed using a variety of approaches. Supertrees build consensus trees from the topological information contained within individual gene trees. Both methods are now widely used and have been demonstrated to solve previously ambiguous or unresolved phylogenies with high statistical support. However, the amount of misleading signal needed to induce erroneous phylogenies for both strategies is still unknown. Using genome simulations, we test the accuracy of supertree and supermatrix approaches in recovering the true organismal phylogeny under increased amounts of horizontally transferred genes and changes in substitution rates. Our results show that overall, supermatrix approaches are preferable when a low amount of gene transfer is suspected to be present in the dataset, while supertrees have greater reliability in the presence of a moderate amount of misleading gene transfers. In the face of very high or very low substitution rates without horizontal gene transfers, supermatrix approaches outperform supertrees as individual gene trees remain unresolved and additional sequences contribute to a congruent phylogenetic signal.

Resumo Limpo

supermatrix supertre analys frequent use accur recov vertic evolutionari histori debat still exist method provid greater reliabl tradit method resolv relationship among organ singl gene often unreli frequent lack strong phylogenet signal presenc systemat artifact method develop reconstruct organism histori multipl gene can divid supermatrix supertre approach supermatrix analysi consist concaten multipl gene singl possibl partit align phylogeni reconstruct use varieti approach supertre build consensus tree topolog inform contain within individu gene tree method now wide use demonstr solv previous ambigu unresolv phylogeni high statist support howev amount mislead signal need induc erron phylogeni strategi still unknown use genom simul test accuraci supertre supermatrix approach recov true organism phylogeni increas amount horizont transfer gene chang substitut rate result show overal supermatrix approach prefer low amount gene transfer suspect present dataset supertre greater reliabl presenc moder amount mislead gene transfer face high low substitut rate without horizont gene transfer supermatrix approach outperform supertre individu gene tree remain unresolv addit sequenc contribut congruent phylogenet signal

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