title: Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects.
abstract: Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.
authors.affiliation: Department of Integrative Zoology, University of Vienna, Vienna, Austria.
authors.forename: Emiliano
authors.initials: E
authors.lastname: Dell'Ampio
authors.forename: Karen
authors.initials: K
authors.lastname: Meusemann
authors.forename: Nikolaus U
authors.initials: NU
authors.lastname: Szucsich
authors.forename: Ralph S
authors.initials: RS
authors.lastname: Peters
authors.forename: Benjamin
authors.initials: B
authors.lastname: Meyer
authors.forename: Janus
authors.initials: J
authors.lastname: Borner
authors.forename: Malte
authors.initials: M
authors.lastname: Petersen
authors.forename: Andre J
authors.initials: AJ
authors.lastname: Aberer
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: Manfred G
authors.initials: MG
authors.lastname: Walzl
authors.forename: Bui Quang
authors.initials: BQ
authors.lastname: Minh
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
authors.forename: Ingo
authors.initials: I
authors.lastname: Ebersberger
authors.forename: Günther
authors.initials: G
authors.lastname: Pass
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D016208:Databases, Factual; D019143:Evolution, Molecular; D023281:Genomics; D060005:Genotyping Techniques / Q000379:methods; D007313:Insecta / Q000145:classification* / Q000235:genetics*; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D059467:Transcriptome
keywords: Collembola; Diplura; ESTs; Ellipura; Entognatha; Nonoculata; Protura; conflicting hypotheses; likelihood quartet mapping; missing data; phylogenomics