02687nas a2200409 4500008004100000245012500041210006900166260001200235300001400247490000600261520162100267653001101888653001401899653001501913653001101928653001401939653001201953653000801965653000901973653001201982653001501994653001202009653002302021653001402044653001402058653001202072653001002084653001002094653001502104653001602119653001502135653002902150653002002179100002002199700001902219856003902238 2013 eng d00aPhylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data0 aPhylotranscriptomics saturated third codon positions radically i c10/2013 a2082-20920 v53 a
"Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions."
10aACTIAS10aANTHERAEA10aBOMBYCIDAE10aBOMBYX10aCERATOMIA10aDARAPSA10aDNA10aENYO10aHEMARIS10aINCOMPLETE10aMANDUCA10aMAXIMUM LIKELIHOOD10aPARSIMONY10aPHYLOGENY10aRADICAL10aRAXML10aSAMIA10aSATURATION10aSATURNIIDAE10aSPHINGIDAE10aSYNONYMOUS SUBSTITUTIONS10aTRANSCRIPTOMICS1 aBreinholt, J.W.1 aKawahara, A.Y. uhttps://doi.org/10.1093/gbe/evt157