Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

Malinsky, Milan; Challis, Richard; Tyers, Alexandra M.; Schiffels, Stephan; Terai, Yohey; Ngatunga, Benjamin P.; Miska, Eric A.; Durbin, Richard; Genner, Martin J.; Turner, George F.

doi:10.1126/science.aac9927

Cited by 368 publications

(516 citation statements)

References 64 publications

Supporting

Mentioning

487

Contrasting

Order By: Relevance

“…This contrasts with findings in Heliconius butterflies where the same loci, associated with similarly few and extreme outlier regions, code for mimicry colour phenotypes across replicate hybrid zones36. The isolation of few loci specific to each contact zone also contrasts with studies implicating a high number of prominent outlier regions hosting candidates under divergent selection associated with the (ecological) contrast in question3738. The apparent difference in number and size of differentiation peaks begs the question on the genetic architecture underlying the trait under selection.…”

Section: Discussionmentioning

confidence: 67%

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

et al. 2016

View full text Add to dashboard Cite

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

show abstract

Section: Discussionmentioning

confidence: 67%

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Ongoing studies may reveal if the sex determination locus on LG5/LG5-14 is the first found both within and without the lake adaptive radiations, and/or shared among radiations. Additionally, a recent report implicated the same region of LG5 as one of a handful of genomic islands of speciation in Astatotilapia species, based on sequence divergence between ecomorphs ([78]; Fig. 2b).…”

Section: Resultsmentioning

confidence: 99%

Polygenic sex determination in the cichlid fish Astatotilapia burtoni

et al. 2016

View full text Add to dashboard Cite

BackgroundThe East African riverine cichlid species Astatotilapia burtoni serves as an important laboratory model for sexually dimorphic physiology and behavior, and also serves as an outgroup species for the explosive adaptive radiations of cichlid species in Lake Malawi and Lake Victoria. An astounding diversity of genetic sex determination systems have been revealed within the adaptive radiation of East African cichlids thus far, including polygenic sex determination systems involving the epistatic interaction of multiple, independently segregating sex determination alleles. However, sex determination has remained unmapped in A. burtoni. Here we present mapping results supporting the presence of multiple, novel sex determination alleles, and thus the presence of polygenic sex determination in A. burtoni.ResultsUsing mapping in small families in conjunction with restriction-site associated DNA sequencing strategies, we identify associations with sex at loci on linkage group 13 and linkage group 5–14. Inheritance patterns support an XY sex determination system on linkage group 5–14 (a chromosome fusion relative to other cichlids studied), and an XYW system on linkage group 13, and these associations are replicated in multiple families. Additionally, combining our genetic data with comparative genomic analysis identifies another fusion that is unassociated with sex, with linkage group 8–24 and linkage group 16–21 fused in A. burtoni relative to other East African cichlid species.ConclusionsWe identify genetic signals supporting the presence of three previously unidentified sex determination alleles at two loci in the species A. burtoni, strongly supporting the presence of polygenic sex determination system in the species. These results provide a foundation for future mapping of multiple sex determination genes and their interactions. A better understanding of sex determination in A. burtoni provides important context for their use in behavioral studies, as well as studies of the evolution of genetic sex determination and sexual conflicts in East African cichlids.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3177-1) contains supplementary material, which is available to authorized users.

show abstract

“…Future studies will indicate whether these lie within a specific genomic region or not, as implicated in ecological speciation of other species, for example, Turner et al. (2005) and Malinsky et al. (2015).…”

Section: Discussionmentioning

confidence: 97%

Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard

2016

View full text Add to dashboard Cite

Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard (Gallotia galloti) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from >20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti. However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.

show abstract

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

Cited by 368 publications

References 64 publications

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Polygenic sex determination in the cichlid fish Astatotilapia burtoni

Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard

Contact Info

Product

Resources

About