Allele Origination by Intergenic Recombination (Adaptive Recursion IV)

ResearchBlogging.orgNew alleles are normally said to arise from mutations, but recombination can be just as potent. Recombination relies on new mutations, of course, but its shuffling power increases the number of possible allele combinations. Biologists Jeffrey Feder and Sebastoam Velez found that the Jamaican click beetles use recombination to generate their unique bioluminescent polymorphisms, but this recombination is between two different, but related, genes, and creates a novel allele cycling system.

Fig. 1: A) Dorsal organs. B) The colors of the green and yellow-green dorsal alleles. C) Ventral organ. D) The colors of the yellow-green, yellow, and orange ventral alleles. From Stolz et al. (2003).

First, a brief review of how bioluminescence works in the Jamaican click beetle, Poryphorus plagiophthalamus. The species has two sets of bioluminescent organs – a pair of dorsal organs and a single ventral organ, and each set’s color is controlled by its own luciferase locus. Within an individual the two sets can be different colors but what makes the species unique, however, is that each organ shows polymorphisms within the species. Related species exhibit only a single color in the ventral locus and another color in the dorsal locus – in P. plagiophthalamus, one can find green or yellow-green dorsal alleles (dGR, dYG) and yellow-green, yellow or orange ventral alleles (vYG, vYE, vOR) (Fig. 1). These alleles are differentiated by point mutations in luciferase that increase or decrease the wavelength.

Gene trees of luciferase indicate that vOR is derived from vYE with only three base substitutions differentiating the two. vYE in turn is derived from vYG (which itself is most likely derived from vGR, as seen in other Poryphorus species). However, Feder and Velez found a (relatively) novel form of allele generation: gene conversion through intergenic recombination, or the imposition of one gene’s sequence (say dorsal) onto another gene’s sequence (ventral). If the right portion of the sequence is converted, a new color allele can be generated.

Stolz et al. first found evidence of intergenic recombination in 2003. Due to most of the found mutations occurring in exon 4 of luciferase (as well as a couple in 1 and 5) and none in exons 2 and 3, the authors could compare evolutionary trees of the exons against each other (Fig. 2).

Fig x: Gene trees of exons in luciferase. On the left, exons 2 & 3 which are not involved in the color phenotype, show different relationships than the color exons 1, 4-7 on the right. On the right, dGR is closely related to vOR/vYE, whereas it is less related on the left. From Stolz et al. (2003).

When they compared the trees, they found incongruence: exons 1, 4-7 in vOR/vYE and dGR (on the right) were more closely related to each other than to exons 2 and 3 (on the left). Because the dorsal and ventral alleles have actually been separated for millions of years, the only way they could be “more related to each other” sequence-wise is by an intergenic recombination event, effectively homogenizing the two genes, which also means that while dorsal and ventral organs are genetically controlled independently, they have not always evolved independently.

The 2003 study did not investigate the effects of intergenic recombination much further but the evolutionary implications were clarified in a 2009 study by Feder and Velez. It turns out that intergenic recombination is relatively common in Poryphorus, being found in several other species. However, due to the polymorphic nature of bioluminescent color in P. plagiophthalamus, intergenic recombination plays a unique role in allele generation.

First, the evidence of recombination. Reconfirming some results in the 2003 study, Feder and Velez found that the dYG and vYG alleles were more closely related to each other than to any other alleles in P. plagiophthalamus (Fig. 3). Also, dYG + vYG/vYE/vOR are nested within a clade containing dGR (Fig. 3). When the dorsal and ventral alleles “should be” nested separately, these results are highly unusual and indicative of intergenic recombination.

Fig. 3: In the red box, the dorsal yellow-green (dYG) allele is more related to the ventral alleles than it is to the dorsal green (dGR) allele. This tree indicates that the ventral alleles are derived from dGR through dYG. From Feder and Velez (2009).

Looking at specific mutations, Feder and Velez were able to construct an evolutionary history of intergenic recombination and allele origins. Evolving from the green allele, the yellow-green allele has two affecting mutations: base-pair 671 has a T->C substitution resulting in a wavelength shift of 14-nm longer (i.e., yellower); base-pair 967 has an A->G transition, shifting wavelength 2-nm longer. Both mutations are found in both dYG and vYG and were likely derived only once, not independently (parsimoniously-speaking) . This is further evidenced by both mutations occurring within sequences already suggested as sites of gene conversion and also by the existence of a silent mutation only found in the dYG/vYG alleles (Feder and Velez 2009).

Because 671C is found in the ventral luciferase locus of both P. plagiophthalamus and P. mellifluous, it is likely that 671C originated in the ventral locus and was later converted over to the dorsal locus in P. plagiophthalamus. The authors propose that 967G, on the other hand, originated in the dorsal locus because dYG is associated with higher genetic diversity and because dYG is more common in Jamaica than is vYG.

Given this evidence, the evolutionary history that Velez and Feder construct is as follows (Fig. 4): the 671C mutation converted from vYE to dGR where it became associated with 967G, causing dGR to mutate to dYG because of the longer wavelength shift. A subsequent dorsal-to-ventral conversion event mutated vYE to vYG. Thus P. plagiophthalamus exhibits a unique system of allele generation: color cycling through intergenic recombination (Fig. 4). Dorsal-to-ventral conversions cause the ventral locus to shift toward shorter wavelengths whereas ventral-to-dorsal conversions cause the dorsal locus to shift toward longer wavelengths. However, the dorsal-to-ventral exchange (longer-to-shorter wavelengths) may be selected against because of possible ongoing selection towards vOR. Here, selection’s role is stopping the cycle from being completely fulfilled.

Fig. 4: The proposed color allele cycling system in P. plagiophthalamus. Dorsal->ventral conversions shift the ventral locus toward green, but due to mutation and subsequent selection towards orange, ventral->dorsal conversions shift the dorsal locus towards longer wavelengths. This cycle is driven by mutation, recombination, and selection. From Feder and Velez (2009).

I find this allele generating system to be incredibly cool. The authors note that intergenic recombination may play similar roles in other biological systems, such as “pathogen-resistant genes in plants, the major histocompatibility complex in mammals, Glutatione S-Transferase genes in Drosophila, silk genes in spiders, and tRNA genes in yeast,” but after reading (or trying to read) those papers, the Jamaican click beetle’s use of intergenic recombination seems to be the simplest.

We have also seen intergenic recombination in the mammalian Y chromosome. The Y chromosome contains multiple copies of many genes that show very high sequence similarity to each other. Thus the Y genes are homogenized through intergenic recombination unlike the polymorphisms of P. plagiophthalamus. This is because the Y’s multiple copies are all fulfilling the same selective purpose – evolving concurrently – whereas the beetle’s dorsal and ventral loci are being pushed in different directions by selection, maintaining different colors. Here, intergenic recombination creates alleles opposed to selective pressures and so polymorphism is maintained. Thus the same mechanism, intergenic recombination, can result in either homogenization of genes or cycling of new alleles – both are neat, but the latter’s dynamism is fascinating!
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Feder JL, & Velez S (2009). Intergenic exchange, geographic isolation, and the evolution of bioluminescent color for Pyrophorus click beetles. Evolution; international journal of organic evolution, 63 (5), 1203-16 PMID: 19154393

Stolz U, Velez S, Wood KV, Wood M, & Feder JL (2003). Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle. Proceedings of the National Academy of Sciences of the United States of America, 100 (25), 14955-9 PMID: 14623957

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