Functional Genomics Offers New Tests of Speciation Hypotheses

Hopkins, David P.; Tyukmaeva, Venera; Gompert, Zachariah; Feder, Jeff; Nosil, Patrik

doi:10.1016/j.tree.2020.08.001

Cited by 10 publications

(9 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Clearly, further work determining the number of loci within inversions and candidate supergenes that contribute to trait variation is warranted. In this regard, emerging techniques that allow functional genetic manipulation of structural variants (e.g., CRISPR‐Cas9) hold promise for making such progress (Hopkins et al, 2020; Kraft et al, 2015).…”

Section: The Supergene Hypothesis: What Is the Evidence For Recombination Suppression Among Loci Controlling Selected Trait Variation?mentioning

confidence: 99%

“…This will yield more precise estimates, but needs to be complemented with functional manipulation in the species with the inversion. Ultimately, functional manipulations such as those offered by CRISPR‐Cas9 may be required to precisely and firmly establish the identities and numbers of variants functionally contributing to trait variation, possibly by “engineering” recombinant alleles to validate the independent effects of individual mutations on a phenotype (Hopkins et al, 2020; Kraft et al, 2015). Such gene editing may be particularly required for identification of causal genetic variation at breakpoints, as many variants will be in complete association in these regions due to the lack of recombination (Hoffmann & Rieseberg, 2008; Matzkin et al, 2005).…”

Section: Future Directionsmentioning

confidence: 99%

See 1 more Smart Citation

Inversion breakpoints and the evolution of supergenes

et al. 2021

Self Cite

View full text Add to dashboard Cite

The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint‐mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.

show abstract

Section: The Supergene Hypothesis: What Is the Evidence For Recombination Suppression Among Loci Controlling Selected Trait Variation?mentioning

confidence: 99%

Section: Future Directionsmentioning

confidence: 99%

Inversion breakpoints and the evolution of supergenes

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Moreover, the use of modern gene editing techniques, especially when combined with feasible ecological and experimental studies, could allow more precise identification of the genes and gene complexes underlying hybrid incompatibilities. For example, CRISPR/Cas9 gene editing technique could be used to revert the X chromosomal inversions in D. montana and D. flavomontana , after which the causal genes for hybrid incompatibilities could be identified through repeated hybridization and resequencing, as suggested by Hopkins et al [ 137 ].…”

Section: Discussionmentioning

confidence: 99%

Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group

Hoikkala

Poikela

2022

Fly

View full text Add to dashboard Cite

Living in high latitudes and altitudes sets specific requirements on species’ ability to forecast seasonal changes and to respond to them in an appropriate way. Adaptation into diverse environmental conditions can also lead to ecological speciation through habitat isolation or by inducing changes in traits that influence assortative mating. In this review, we explain how the unique time-measuring systems of Drosophila virilis group species have enabled the species to occupy high latitudes and how the traits involved in species reproduction and survival exhibit strong linkage with latitudinally varying photoperiodic and climatic conditions. We also describe variation in reproductive barriers between the populations of two species with overlapping distributions and show how local adaptation and the reinforcement of prezygotic barriers have created partial reproductive isolation between conspecific populations. Finally, we consider the role of species-specific chromosomal inversions and the X chromosome in the development of reproductive barriers between diverging lineages.

show abstract

“…More recently, it has been reported that chromosomal rearrangements can also affect gene regulation by disrupting higher-order chromatin organization [121]. However, the recombination suppression has made it difficult to apply conventional genetic analyses, such as fine mapping using recombinants, to further narrow down the candidate genes and mutations [122].…”

Section: Targeted Induction Of Chromosomal Rearrangementsmentioning

confidence: 99%

Speciation and adaptation research meets genome editing

Ansai

Kitano

2022

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

show abstract

Functional Genomics Offers New Tests of Speciation Hypotheses

Cited by 10 publications

References 12 publications

Inversion breakpoints and the evolution of supergenes

Inversion breakpoints and the evolution of supergenes

Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group

Speciation and adaptation research meets genome editing

Contact Info

Product

Resources

About