ArticleBMC evolutionary biology2020
Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes.
Article in BMC evolutionary biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.Genome research · 2025Article
- Structural Variants and Speciation: Multiple Processes at Play.Cold Spring Harbor perspectives in biology · 2024Review
- A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish.Ecology and evolution · 2022Article
- Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing.Frontiers in genetics · 2021Article
- Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes.Genome biology and evolution · 2019Article
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5 authors.
Funding
Abstract
backgroundEast African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa.
resultsHere, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with "antigen processing and presentation" and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events.
conclusionsAltogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.
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