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Even though the existence of inversions during primate evolution and speciation has been long known [ 23, 24], we still lack a complete picture of how many polymorphic inversions exist in the human genome and their association with changes in gene expression, adaptation or disease.
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In humid forested regions, polymorphisms are nearly absent and the standard (uninverted) arrangements prevail, whereas Guinea and Sudan savanna populations are characterized by many highly polymorphic inversions [ 5, 11, 14].
To date, associations between inversion alleles and gene expression have been performed only for a few of the most studied human polymorphic inversions for which it was possible to predict the genotypes in many individuals [ 44, 85, 105].
Our knowledge of inversion polymorphisms is mostly restricted to D. buzzatii, in which polymorphic inversions are known to affect morphological and fitness related traits (see [ 52] and references therein).
The traits recovery of Jalmagna was due to integration of many polymorphic markers in the backcross breeding program.
However, a striking pattern found in An. gambiae is the overrepresentation of polymorphic inversions on chromosome 2R.
Although this arm represents <30% of the polytene complement, it carries 58% of all polymorphic inversions [21].
Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii.
Following this criterion, haplotype subgroups can be defined in polymorphic inversions because different alleles are maintained in the different orientations.
In Drosophila, this process has been responsible for most of the inversions fixed between D. melanogaster and D. yakuba [43] as well as three D. melanogaster polymorphic inversions [44] [46].
We have previously found that the cut-and-paste transposon Galileo was involved in the generation of two polymorphic inversions of D. buzzatii, 2j and 2q7 [38], [38].
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