The East African Lake Malawi haplochromine cichlid flock represents one of the largest and most diverse adaptive radiations on earth, with over 700 species of fish. It is an important model system with which to understand ecological diversification, sexual selection and speciation. Our analyses focused on four sympatric species of the endemic deep-water genus Diplotaxodon (fig. 1), previously found to differ significantly in morphology and male monochromatic nuptial color [1] and proposed as an example of sympatric speciation. Introduc)on Single digest RADseq (SbfI) 50 individuals; ~3.5M reads/ind 5 populations > 8 individuals per pop Methods Genomic diﬀeren)a)on among deep-­‐water cichlid species References The genomic architecture of speciation in the Lake Malawi deep water cichlid genus Diplotaxodon Christoph Hahn & Domino Joyce School of Biological, Biomedical and Environmental Sciences, University of Hull 1. Genner et al. 2007. MolEcol. 2. Catchen et al. 2013. MolEcol. 3. Jombart & Ahmed 2011. Bioinformatics. 4. Brawand et al. 2014. Nature. 5. Conesa & Goetz. 2008. Int. J. Plant Gen. 6. Foll & Gaggiotti. 2008. Genetics. 7. Coop et al. 2010. Genetics. @EvoHull https://github.com/chrishah Acknowledgements This is a collaboration with Dr Martin Genner, and is funded by NERC grant number NE/ K000829/1. Principal data processing using STACKS [2], adegenet [3] and custom scripts (https://github.com/chrishah). Genome scans are based on the recently published genome of Metriaclima zebra [4]. Functional annotation of genes obtained using Blast2GO [5]. Fig. 2: Number of candidate outlier loci identified using STACKS [1], BayeScan [6], and Bayenv2 [7]. . Fig. 1: Principal component analysis (PCA) based on > 25,000 SNPs, differentiating the 4 putative Diplotaxodon species. . We used Principal Component scores (PC1) inferred from morphological data in [1] as proxy to specifically identify genomic regions associated with morphological differentiation between species (fig. 3). Normalized P C 1 s c o r e s w e r e u s e d a s ‘environmental factors’ in Bayenv2 [7]. Fig 3: Transformed bayes factor ranks averaged across 10 independent Bayenv2 runs. The vertical red line delimits the 95th average rank percentile as threshold for candidate loci. The inset shows the species wide PC1 scores [1] used as ‘environmental factors’ in the analyses. Divergent genomic regions between Diplotaxodon species are enriched for genes controlling craniofacial- eye development (see fig. 4). Our results indicate that the increasingly narrow, short wave- length light-spectra at greater water depths pose unique selective constraints and are likely key drivers of ecological and sexual selection and ultimately speciation in this group of Lake Malawi cichlids. Fig 4: (A-F) Pairwise divergence (FST) across three selected scaffolds. Displayed are observed values and kernel smoothed averages. Red dots represent candidate outlier loci identified by STACKS (p < 5e-7). Y axes range 0 < FST < 1. (A) Di_1 vs Di_2; (B) Di_1 vs Di_4; (C) Di_1 vs Di_5; (D) Di_2 vs Di_4; (E) Di_2 vs Di_5; (F) Di_4 vs Di_5. (G) Average transformed ranks inferred from the ‘morphology informed’ Bayenv analyses (fig. 3). Red dots represent average ranks in the 95th percentile. D. limnothrissa black pelvic (Di_2) D. macrops black dorsal (Di_1) D. macrops ngulube (Di_5) D. macrops offshore (Di_4) c.hahn@hull.ac.uk A B C D E F G Fig. 4 (contd): Rectangles at the bottom represent genes within 15kb windows of candidate outlier SNPs (craniofacial- or eye development). X axes scale: 100kb/tick. Find it on figshare