High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Abstract

Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (F ST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.

Harnessing the power of RADseq for ecological and evolutionary genomics

“…Hohenlohe et al 20 used RADseq to identify 3180 species-diagnostic SNPs and calculate admixture between a native and an invasive trout species; see also Eaton & Ree 2013 82 , Ford et al 2015 83 .…”

Eco‐morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa

“…; Ford et al . ). Knowledge about the amount of gene flow is essential for the interpretation of population divergence and to draw informed inferences of how this will be reflected at the genomic level (Feder et al .…”

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

“…They address some of the most hotly debated evolutionary radiations in animals and plants, including cichlids (e.g. Schliewen et al 2001;Colombo et al 2013;Keller et al 2013;Manousaki et al 2013;Albertson et al 2014;Ford et al 2015), sticklebacks (Gow et al 2006;Berner et al 2010;Deagle et al 2013;Feulner et al 2013), Anolis lizards (Glor et al 2005;Ng & Glor 2011;Muñoz et al 2013), Heliconius butterflies (Nadeau et al 2013), Darwin 0 s finches (Petren et al 2005), plants of the Hawaiian silversword alliance (Lawton-Rauh et al 2007), oak trees (Cavender-Bares et al 2015) and bromeliads (Palma-Silva et al 2011). Due to the targeted nature of our search and the specific search terms used, our literature review is certainly not exhaustive.…”