Inversions maintain differences between migratory phenotypes of a songbird

Lundberg, Max; Mackintosh, Alexander; Petri, Anna; Bensch, Staffan

doi:10.1038/s41467-023-36167-y

Cited by 12 publications

(10 citation statements)

References 107 publications

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“…Useful evidence includes the probability of gene tree discordance estimated from polymorphism data (Dutheil et al . 2009), as well as whether rearrangement break points are consistent with multiple origins (Lundberg et al . 2023).…”

Section: Discussionmentioning

confidence: 99%

Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny

Mackintosh,

de la Rosa,

Martin

et al. 2023

Preprint

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Chromosome rearrangements shape the structure of the genome and influence evolutionary processes. Inferring ancestral chromosomes and rearrangements across a phylogenetic tree is therefore an important analysis within evolutionary genetics. One approach to this inference problem is to focus on synteny information, i.e. the co-occurrence of loci on the same chromosome. Although algorithms for inferring ancestral linkage groups (ALGs) and inter-chromosomal rearrangements from synteny have been previously described, they have seldom been applied to modern genome data. Here we implement these algorithms in a command-line tool, syngraph, and evaluate their performance using simulations that include a mix of different rearrangements and types of error. We show that ALGs and rearrangements can be recovered when the rearrangement frequency per-branch is well below the number of chromosomes. We demonstrate that competing models of rearrangement can be inferred by comparing observed results to simulations. Finally, we reanalyse genome assemblies of rhabditid nematodes and find that independent fusions of the same ALGs pose a challenge that is difficult to overcome without gene-order information. Our simulations and analysis of real data demonstrate both the promise and limitations of using synteny information to infer patterns of genome evolution.

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Section: Discussionmentioning

confidence: 99%

Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny

Mackintosh,

de la Rosa,

Martin

et al. 2023

Preprint

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“…Delmore et al 2023;Knief et al, 2019). Lundberg et al, 2023). The same trait can be modified in multiple ways, as a 710-bp deletion on chromosome 27 in the Eurasian Blackcap (Sylvia atricapilla) also shapes migratory phenotypes (Delmore et al, 2023).…”

Section: S Vs/phenot Ype a Sso Ciati On S In Non -Model B Irdsmentioning

confidence: 99%

How structural variants shape avian phenotypes: Lessons from model systems

Recuerda,

Campagna

2024

Molecular Ecology

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Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long‐read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short‐read sequencing and associated analytical methods. SVs most commonly involve non‐coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co‐occur with single‐nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long‐read technologies become commonly implemented in non‐model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

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“…At least 49 unique inversions have now been linked to adaptive phenotypic traits in Anopheles mosquitoes (19). Inversions have been shown to control the phenotypes underlying mimicry in butterflies (15,16,20) as well as mating and migratory behaviors in birds (21)(22)(23)(24). Shifts in the frequency of inversion polymorphisms have been linked to adaptation to forest versus prairie habitats in deer mice (25) and to global climate change in Drosophila (26,27).…”

Section: Introductionmentioning

confidence: 99%

The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower,Mimulus guttatus

Kollar,

Stanley,

Kenchanmane Raju

et al. 2023

Preprint

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Large chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a large role in the evolution of adaptations in those species. Despite their importance, the underlying mechanisms by which inversions produce their adaptive phenotypic effects and become geographically widespread are still poorly understood. One way inversions could cause phenotypic effects is through meiotic recombination suppression, which can result in the formation of a supergene containing linked adaptive alleles. This supergene hypothesis has been promoted by theoreticians, but thus far, no studies have definitively identified multiple linked adaptive genes within an inversion. Alternatively, according to the breakpoint mutation hypothesis, the inversion mutation itself could result in adaptive phenotypic effects if it disrupts genes or alters regulation of nearby genes. Here, we evaluate both of these hypotheses using new long-read sequencing-based genomes of the yellow monkey flower,Mimulus guttatus. Our results provide support for both the supergene and breakpoint mutation hypotheses of adaptive inversion evolution and suggest that functional molecular studies will be required to definitively test each of these hypotheses. We also identified an ancient large inversion nested within a well-established adaptive inversion. This finding suggests that the supergene mechanism may occur in phases, with an expansion of the region of suppressed recombination capturing an increasing number of adaptive loci over time.Significance statementLarge regions of chromosomes can become reversed in orientation due to mutations known as inversions. These inversions are often involved in the evolution of major organismal adaptations, yet we know little about this process. In this study, we show that the evolution of a large adaptive inversion in monkeyflowers could be due to both the trapping of beneficial genes into a supergene as well as changes in gene expression due to the inversion mutation itself. Further, we found that this inversion has trapped an even older inversion, which may itself have been adaptive. Thus, adaptive inversions on autosomes may evolve in sequence, much the same way that sex chromosomes evolve.

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Inversions maintain differences between migratory phenotypes of a songbird

Cited by 12 publications

References 107 publications

Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny

Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny

How structural variants shape avian phenotypes: Lessons from model systems

The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower,Mimulus guttatus

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