1. Complex phylogenetic relationships among sand-dwelling Malawi cichlids.
Complex phylogenetic relationships among sand-dwelling Malawi cichlids. (A) We plotted 1,927 phylogenies resulting from nonoverlapping 10,000 SNP windows using DensiTree. The consensus phylogeny produced by DensiTree is colored black. (B) Bar plot of mean genome-wide weightings for the 15 tree topologies tested with Twisst. Trees grouping clades by bower phenotype (topologies 15, 10, and 3) are highlighted. See SI Appendix, Fig. S4 for visualizations of all 15 topologies. (C) An example of a stacked plot of topology weightings along a region of LG11 with strong support for groupings by phenotype. (D) An example of a stacked plot of a mixed-weight region on LG10. (E) Heatmap of the most significant f4 values. Species in the x and y axes were either B or C in the form f4(A,B;C, A. calliptera). Names of pit-digging and castle-building species are in blue and red font, respectively. A darker red square indicates more signal of gene flow between the species pairs in the respective row and column.
Ryan A. York et al. PNAS 2018;115:47:E11081-E11090
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