Inversions and Evolution

Abstract

Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.

Key Concepts

  • Inversions are chromosomal rearrangements where the order of loci is reversed.
  • Inversions can be under negative, positive or balancing selection.
  • A key effect is that they reduce recombination in individuals heterozygous for the arrangement.
  • They therefore facilitate the maintenance of ‘blocks’ of associated alleles.
  • This is favourable under local adaptation, positive epistasis and frequency‐dependent selection favouring multiple different morphs in a population.
  • Accordingly, inversions have been shown to contribute to the maintenance of within‐species polymorphism and between‐species divergence in various empirical studies.
  • Inversions also contribute to speciation by coupling different barriers to gene flow.
  • Finally, they also contribute to sex‐chromosome differentiation and degeneration.
  • Identifying the targets of selection within inversion is challenging but possible, at least for old inversions.
  • Knowing the evolutionary history of inversions is fundamental to understanding their influence in adaptation and speciation.

Keywords: chromosomal rearrangements; recombination; local adaptation; speciation; balancing selection; polymorphism; sex chromosomes

Figure 1. Inversions are changes in the orientation of a section of a chromosome that might be entirely within one chromosome arm (paracentric) or might include the centromere (pericentric). They give rise to two alternative arrangements: standard and inverted.
Figure 2. After a new inversion arises by mutation, it can be subject to multiple forms of selection either due to breakpoint effects or due to the sets of alleles held together in the alternative arrangements by suppressed recombination. See text for discussion of these forms of selection, which may occur alone or in combination.
Figure 3. Detection of an inversion (delimited by dark red vertical bars) in a target sample by comparison with a reference genome using read‐pair and split‐read approaches. Reads from a target sample are mapped against the reference genome (of the same or a closely related species) with the standard arrangement, to identify changes in position, orientation and contiguity, when compared to the genome of the target sample (generally not available, here with the inverted arrangement). Based on the read‐pair approach, an inversion is detected when read pairs mapping to each side of the breakpoints (black and white read pairs) show a different orientation (arrow directions) and distance from each other when mapped against the reference genome. The split‐read approach detects inversions by identifying long reads (dark grey) that ‘split’ into two different ‘pieces’ with opposing orientation when mapped against the reference genome. Multiple independent reads supporting the same inversion are generally required to reduce false positives.
Figure 4. Gene flux, which has strong effects away from inversion breakpoints (dark red vertical lines), can generate a ‘suspension bridge’ pattern of genetic differentiation between inversion arrangements. The expected pattern is shown for (a) high gene flux without loci involved in local adaptation within the inversion; (b) low gene flux without loci involved in local adaptation within the inversion and (c) high gene flux with two outstanding divergence peaks at loci involved in local adaptation within the inversion (green arrows).
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Further Reading

Coyne JA and Orr HA (2004) Speciation. Sinauer Associates Sunderland: MA.

Faria R and Navarro A (2010) Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends in Ecology & Evolution 25: 660–669.

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Jackson B, Butlin R, Navarro A and Faria R (2016) Speciation, chromosomal rearrangements and. In: Kliman RM (ed.) Encyclopedia of Evolutionary Biology, pp 149–158. Academic Press: Oxford.

Kemppainen P, Knight CG, Sarma DK, et al. (2015) Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Molecular Ecology Resources 15: 1031–1045.

Smadja CM and Butlin RK (2011) A framework for comparing processes of speciation in the presence of gene flow. Molecular Ecology 20: 5123–5140.

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Westram, Anja M, Faria, Rui, Butlin, Roger, and Johannesson, Kerstin(May 2020) Inversions and Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0029007]