Understanding explosive diversification through cichlid fish genomics

Abstract

Owing to their taxonomic, phenotypic, ecological and behavioural diversity and propensity for explosive diversification, the assemblages of cichlid fish in the East African Great Lakes Victoria, Malawi and Tanganyika are important role models in evolutionary biology. With the release of five reference genomes and many additional genomic resources, as well as the establishment of functional genomic tools, the cichlid system has fully entered the genomic era. The in-depth genomic exploration of the East African cichlid fauna — in combination with the examination of their ecology, morphology and behaviour — permits novel insights into the way organisms diversify.

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Fig. 1: The species flocks of cichlid fish in East Africa.
Fig. 2: The Tropheus species complex from Lake Tanganyika.
Fig. 3: Phylogenetic inference in rapidly diversifying clades.
Fig. 4: Phylogenetic relationships among the cichlid faunas in the East Africa Great Lakes Victoria, Malawi and Tanganyika.

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Acknowledgements

The author is grateful for generous support from the European Research Council (ERC) and the Swiss National Science Foundation (SNF) and to three referees for valuable comments.

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Nature Reviews Genetics thanks G. F. Turner and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Glossary

Model organisms

Non-human species studied in detail in the context of a particular research question with the motivation to be able to make more general statements about the functioning of organisms.

Clades

Branches on an evolutionary tree, consisting of a common ancestor and all its descendants (a clade is, hence, equivalent to a monophyletic group).

Divergence mapping

Genetic-marker-based search for genomic regions exhibiting exceptionally strong differentiation between different biological entities, such as populations or species.

Species flocks

Unusually taxon-rich assemblages of closely related species that coexist in the same area, such as an island, a lake or a section of a river.

Lateral line

A sensory system along the body in aquatic vertebrates that consists of sensory cells.

Sympatry

The existence of two or more species in the same geographic area such that they encounter each other frequently.

Reproductive isolation

Any property that prevents (or reduces the probability of) members of one species breeding successfully with members of another species.

Gene flow

The movement or exchange of genes into or through a population by interbreeding or by migration and subsequent interbreeding.

Speciation continuum

The bandwidth of variation between diversifying populations ranging from virtually no variation (panmixia) through partially discontinuous variation (incipient barriers to gene flow) to strongly discontinuous variation (complete reproductive isolation).

Tribes

The taxonomic rank between the genus and the family level.

Sister taxa

Reciprocally closest relatives of one another.

Ring species

Two reproductively isolated populations are connected through a geographic ring of populations that interbreed; no morphological character can be used, except arbitrarily, to divide the ring into discrete taxonomic units.

Biological species concept

A concept positing that species are groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups.

Haplotype

A stretch of DNA on a single molecule (chromosome, plastid or mitochondrion) that is inherited as a single unit.

Phylogenetic species concept

A concept positing that species are ‘tips’ on a phylogeny, that is, the smallest set of organisms that share an ancestor and can be distinguished from other such sets.

Monophyly

The condition of forming a monophyletic group (that is, a clade).

Ecological species concept

A concept positing that species are sets of organisms that are adapted to a particular set of resources, that is, to the same ecological niche.

Incomplete lineage sorting

The imperfect segregation of a gene into all evolutionary lineages, that is, a gene fails to coalesce within the duration of a species.

Introgression

Also referred to as introgressive hybridization. The transfer of genetic material from one species into another via repeated and asymmetrical backcrossing with one of the parental lineages after a hybridization event.

Mosaic genomes

Genomes heterogeneous in ancestry, emerging from introgression, incomplete lineage sorting or lateral gene transfer.

Gene trees

Actual evolutionary relationships between the versions of a gene as present in different taxa.

Species tree

Actual evolutionary relationships between a set of species. The species tree reflects the ‘true’ evolutionary history of a clade.

Ecological opportunity

The availability of ecologically accessible resources that may be exploited by an evolutionary lineage.

Trio sequencing

Whole-genome sequencing of two parents and one of their offspring, allowing accurate phasing (and the determination of the nucleotide mutation rate if sequence coverage is high enough).

Syndrome selection

Selection on a combination of traits (for example, body and mouth morphology and coloration in cichlids) in a given environment.

F ST

Known as the fixation index, FST is a measure of differentiation between two populations due to genetic structure.

D XY

Average number of differences between two individuals randomly sampled from two populations.

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Salzburger, W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 19, 705–717 (2018). https://doi.org/10.1038/s41576-018-0043-9

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