The genomic substrate for adaptive radiation in African cichlid fish

Abstract

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

The puzzling phylogeography of the haplochromine cichlid fishAstatotilapia burtoni

“…The obtained RADseq reads were quality filtered, sorted according to barcode, and aligned to the A. burtoni reference genome (release Broad HapBur1.0, Brawand et al., 2014; using novoalign v2.08.03 (http://novocraft.com). The alignment score was set to 200 with a default gap‐opening penalty and a gap extend penalty of 15 accepted (parameters implemented for the alignment: ‐F STDFQ ‐t200 ‐g40 ‐×15 ‐oSAM ‐oFullNW –3Prime ‐rN ‐e10 –f) (see Egger et al., 2017).…”

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…This method is popular and has been used in many studies since its inception (Figure S1). RAD sequencing has been used, particularly in fish, to identify population divergence (Boehm, Waldman, Robinson, & Hickerson, 2015; Ferchaud & Hansen, 2016; Larson et al., 2014), for SNP identification in polyploid fish (Hohenlohe, Amish, Catchen, Allendorf, & Luikart, 2011; Ogden et al., 2013; Palti et al., 2014), in phylogeographic studies (Macher et al., 2015; Reitzel, Herrera, Layden, Martindale, & Shank, 2013), for QTL analysis (Gagnaire, Normandeau, Pavey, & Bernatchez, 2013; Houston et al., 2012; Yoshizawa et al., 2015), for linkage mapping (Brieuc, Waters, Seeb, & Naish, 2014; Henning, Lee, Franchini, & Meyer, 2014), in hybridization studies (Hand et al., 2015; Lamer et al., 2014; Pujolar et al., 2014), for exploration of genome architecture and evolution (Brawand et al., 2014; Kai et al., 2014; Waples, Seeb, & Seeb, 2016), and in phylogenetic analyses (Gonen, Bishop, & Houston, 2015; Wagner et al., 2013). This methodology should be particularly suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not easily visible in traditional analyses based on relatively few loci (Davey et al., 2011).…”

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

“…In ecological genomics of fishes more generally, stickleback fishes (genome size 675 Mb) are now often whole genome resequenced (Jones et al, 2012;Terekhanova et al, 2014) as are some cichlids (genome size *1 Gb) either with few individuals at high coverage (e.g. Brawand et al, 2014) or with individuals pooled and overall lower coverage focusing on fixed differences (e.g. Elmer et al, 2014).…”