2021
DOI: 10.1093/molbev/msab151
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Abstract: Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing th… Show more

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Cited by 59 publications
(48 citation statements)
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“…2B). However, a careful dissection of these signals shows that loci with high phylogenetic usefulness (as defined by [3, 37]; see Methods) favor the topology shown in Fig. 2A, with the morphological hypothesis becoming dominant only after incorporating less reliable loci (Fig .2C).…”
Section: Resultsmentioning
confidence: 99%
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“…2B). However, a careful dissection of these signals shows that loci with high phylogenetic usefulness (as defined by [3, 37]; see Methods) favor the topology shown in Fig. 2A, with the morphological hypothesis becoming dominant only after incorporating less reliable loci (Fig .2C).…”
Section: Resultsmentioning
confidence: 99%
“…Given conflicts between methods in the resolution of one particular node (involving the relationships among Arbacioida, Salenioida, and the clade of Stomopneustoida + Camarodonta), all methods were repeated after reducing the matrix to 500 and 100 loci selected for their phylogenetic usefulness using the approach described in [3, 37] and implemented in the genesortR script (https://github.com/mongiardino/genesortR). This approach relies on seven gene properties routinely used for phylogenomic subsampling, including multiple proxies for phylogenetic signal—such as the average BS and Robinson-Foulds (RF) similarity to a target topology—as well as several potential sources of systematic bias (e.g., rate and compositional heterogeneities).…”
Section: Methodsmentioning
confidence: 99%
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