Evolutionary Biology

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

10.24072/pcjournal.172 - Peer Community Journal, Volume 2 (2022), article no. e54.

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Human-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.

Published online:
DOI: 10.24072/pcjournal.172
Fraïsse, Christelle 1, 2; Le Moan, Alan 3, 4; Roux, Camille 1; Dubois, Guillaume 3; Daguin-Thiebaut, Claire 3; Gagnaire, Pierre-Alexandre 2; Viard, Frédérique 2, 3; Bierne, Nicolas 2

1 CNRS, Univ. Lille, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France
2 ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
3 CNRS UMR 7144 - Sorbonne University, 29680 Roscoff, France
4 Department of Marine Sciences, Tjärnö Marine Laboratory, Gothenburg University, 452 96 Strömstad, Sweden
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     title = {Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?},
     journal = {Peer Community Journal},
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     publisher = {Peer Community In},
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%A Le Moan, Alan
%A Roux, Camille
%A Dubois, Guillaume
%A Daguin-Thiebaut, Claire
%A Gagnaire, Pierre-Alexandre
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Fraïsse, Christelle; Le Moan, Alan; Roux, Camille; Dubois, Guillaume; Daguin-Thiebaut, Claire; Gagnaire, Pierre-Alexandre; Viard, Frédérique; Bierne, Nicolas. Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?. Peer Community Journal, Volume 2 (2022), article  no. e54. doi : 10.24072/pcjournal.172. https://peercommunityjournal.org/articles/10.24072/pcjournal.172/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100149

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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