Abstract
BackgroundInversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Some insect species have evolved mechanisms to reduce the cost of embryo mortality but humans have not. In birds, a detailed analysis is missing although intraspecific inversion polymorphisms are regarded as common. In Australian zebra finches (Taeniopygia guttata), two polymorphic inversions are known cytogenetically and we set out to detect these two and potentially additional inversions using genomic tools and study their effects on embryo mortality and other fitness-related and morphological traits.ResultsUsing whole-genome SNP data, we screened 948 wild zebra finches for polymorphic inversions and describe four large (12–63 Mb) intraspecific inversion polymorphisms with allele frequencies close to 50 %. Using additional data from 5229 birds and 9764 eggs from wild and three captive zebra finch populations, we show that only the largest inversions increase embryo mortality in heterokaryotypic males, with surprisingly small effect sizes. We test for a heterozygote advantage on other fitness components but find no evidence for heterosis for any of the inversions. Yet, we find strong additive effects on several morphological traits.ConclusionsThe mechanism that has carried the derived inversion haplotypes to such high allele frequencies remains elusive. It appears that selection has effectively minimized the costs associated with inversions in zebra finches. The highly skewed distribution of recombination events towards the chromosome ends in zebra finches and other estrildid species may function to minimize crossovers in the inverted regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1056-3) contains supplementary material, which is available to authorized users.
Highlights
Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa
Some parts of the genome assembly are missing at this position [57, 58], yet crossovers between the centromere and a marker located within the linkage disequilibrium (LD) region occur in heterokaryotypic individuals [57] and we conclude that the LD region does not cover the centromere (Table 1)
Large inversion polymorphisms are abundant in the estrildid finch family [45,46,47]
Summary
Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Genetic polymorphisms range in size from single nucleotides (SNPs) to large scale insertions, deletions, or rearrangements that span several millions of base pairs [1, 2] Among these structural variants, inversions play a prominent role and have long been recognized as drivers of local adaptation and speciation (reviewed in [3]). In heterokaryotypic individuals (those that are heterozygous for an inversion) recombination within the inverted region is largely suppressed, either because homologous pairing is partially inhibited or because crossovers give rise to unbalanced gametes (carrying deletions or duplications) which will lead to the death of the zygote [1] These two processes are not mutually exclusive and their prevalence depends, amongst others, on the size and location of the inverted region [5,6,7,8]. A single crossover within a pericentric inversion leads to the formation of two chromatids with duplications and deficiencies and two normal chromatids, whereas in paracentric inversions an acentric fragment and a dicentric chromatid
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