Testing for a role of postzygotic incompatibilities in rapidly speciated Lake Victoria cichlids

Intrinsic postzygotic hybrid incompatibilities are usually due to negative epistatic interactions between alleles from different parental genomes. While such incompatibilities are thought to be uncommon in speciation with gene flow, they may be important if such speciation results from a hybrid population. Here we aimed to test this idea in the endemic cichlid fishes of Lake Victoria. Hundreds of species have evolved within the lake in <15k years from hybrid progenitors. While the importance of prezygotic barriers to gene flow is well established in this system, the possible relevance of postzygotic genetic incompatibilities is unknown. We inferred the presence of negative epistatic interactions from systematic patterns of genotype ratio distortions in experimental crosses and wild samples. We then compared the positions of putative incompatibility loci to regions of high genetic differentiation between sympatric sister species as well as between members of clades that may have arise..., , , # Testing for a role of postzygotic incompatibilities in rapidly speciated Lake Victoria cichlids

[https://doi.org/10.5061/dryad.ksn02v7bf]()

## F2 hybrid CROSS information (species used as female x species used as male)

PNPxPPP stands for the cross between Pundamilia sp. \"nyererei-like\" and Pundamilia sp. \"pundamilia-like\"
PPMxPRHZ stands for the cross between Pundamilia pundamilia and Pundamilia sp. \"red-head\"
PNPxNOM stands for the cross between Pundamilia sp. \"nyererei-like\" and Neochromis omnicaeruleus

## Analysis steps with list of input and output files

### CROSSES

#### 1. filter cross VCF files using \"Crosses\_VCF\_filtering.txt\"

###### input: the unfiltered cross VCF files:

* PNPxNOM_7more.vcf.gz -> originally from Feller et al. 2022,
* PNPxPPP_final.vcf.gz -> originally from Feller et al. 2020,
* PPMxPRHZ.vcf.gz -> originally from Feller et al. 2020,

###### output: the quality filtered, phased\&imputed, and subsetted VCF files (grandparental g...