Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations ofNicaraguan crater lake cichlid fishes

Abstract

Divergent selection is the main driving force in sympatric ecological speciation and may also play a strong role in divergence between allopatric populations. Characterizing the genome-wide impact of divergent selection often constitutes a first step in unravelling the genetic bases underlying adaptation and ecological speciation. The Midas cichlid fish (Amphilophus citrinellus) species complex in Nicaragua is a powerful system for studying evolutionary processes. Independent colonizations of isolated young crater lakes by Midas cichlid populations from the older and great lakes of Nicaragua resulted in the repeated evolution of adaptive radiations by intralacustrine sympatric speciation. In this study we performed genome scans on two repeated radiations of crater lake species and their great lake source populations (1030 polymorphic AFLPs, n ∼ 30 individuals per species). We detected regions under divergent selection (0.3% in the crater lake Xiloá flock and 1.7% in the older crater lake Apoyo radiation) that might be responsible for the sympatric diversifications. We find no evidence that the same genomic regions have been involved in the repeated evolution of parallel adaptations across crater lake flocks. However, there is some genetic parallelism apparent (seven out of 51 crater lake to great lake outlier loci are shared; 13.7%) that is associated with the allopatric divergence of both crater lake flocks. Interestingly, our results suggest that the number of outlier loci involved in sympatric and allopatric divergence increases over time. A phylogeny based on the AFLP data clearly supports the monophyly of both crater lake species flocks and indicates a parallel branching order with a primary split along the limnetic-benthic axis in both radiations.

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

“…This agrees with previous research that did not identify parallel signals of genomic response to selection across these radiations 29 . It also may suggest a degree of predictability in divergence along the benthic-limnetic axis that might overcome particular lake-specific populationspecific historical and demographic effects when a new and depauperate habitat is colonized.…”

“…6). Perhaps because of the larger complement of species and genomic data in the current study, this differs from a previous genetic analysis that found A. sagittae to be the first divergence in Xiloá 29 .…”

Pronounced genetic differentiation of small, isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya

“…This time may have been sufficient to have allowed populations in individual lagoons to differentiate and diverge into unique populations. Similar time period has been found in Crater Lake cichlids in Nicaragua, to be sufficient even for the origin of new species (Barluenga et al, 2006;Kautt et al, 2012). Although the route and timing of the colonisation history of the Magadi-Natron lake basin remains unclear, several periods of high water levels have been reported within the entire soda lake region and could have provided opportunities for exchange of fish between the three lakes.…”

Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish?

“…2004; Kautt et al. 2012; Machado‐Schiffiano et al. 2015), determining both the source species and factors structuring the introgression of hybrid genotypes could be difficult (Mims et al.…”