Computational protocol: Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish☆

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Protocol publication

[…] PAUP 4.05b () was used to construct a neighbor joining (NJ) tree based on Nei-Li distances () and estimate statistical support from 1000 bootstrap replicates. To test for effects of outgroup composition, analyses were conducted with only ingroup taxa (the “ingroup dataset”) and with eight different sets of outgroup taxa, i.e. the “full dataset” using the complete outgroup (17 taxa from six tribes, encompassing the diversity of the entire C-lineage), and seven datasets with smaller outgroups (Ectodini; a monophyletic clade of Perissodini + Benthochromini + Cyprichromini; Cyprichromini; Benthochromini; Perissodini; Cyphotilapiini; Tropheini). For the ingroup dataset, a Neighbor-Net analysis based on a distance matrix was conducted in SplitsTree v.4.10 () as an explorative approach for identifying conflicting phylogenetic signal in the data.To test for consistency between mtDNA- and AFLP-based tree topologies, we evaluated the fit of the mtDNA sequence data () to the unrooted NJ tree topology derived from ingroup AFLP data, by constraining a maximum likelihood (ML) tree search with the substitution model GTR + I + G () to the AFLP tree. The Shimodaira-Hasegawa (SH) test (; full optimization, 10,000 bootstrap replicates; implemented in PAUP) was then used to test whether the likelihood of the mtDNA data was significantly lower under the AFLP-NJ topology than under an unconstrained topology optimized from the mtDNA data. […]

Pipeline specifications

Software tools PAUP*, SplitsTree
Application Phylogenetics
Organisms Hemisus marmoratus