Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?use asterix (*) to get italics

Christelle Fraïsse, Alan Le Moan, Camille Roux, Guillaume Dubois, Claire Daguin-Thiébaut, Pierre-Alexandre Gagnaire, Frédérique Viard, Nicolas BiernePlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2022

<p style="text-align: justify;">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, <em>Ciona robusta</em>, has been recently introduced in the native range of its sister taxa, <em>Ciona intestinalis</em>, 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 <em>C. intestinalis </em>and <em>C. robusta</em> 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 <em>C. robusta</em> haplotypes segregating in <em>C. intestinalis</em>, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, <em>C. robusta</em> 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.</p>

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ascidians, trio-based genome phasing, anthropogenic hybridization, introgression hotspot, cytochrome P450

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Adaptation, Hybridization / Introgression, Population Genetics / Genomics

Markus Möst: ecological adaptation and speciation in the face of gene flow. University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, AUSTRIA. [markus.moest@uibk.ac.at], Erin Calfee: genomics, statistical methods to infer selection after admixture. University of California, One Shields Avenue, Davis, CA 95616, USA [erincalfee@gmail.com], Henry North: genomics, adaptive introgression, spread of invasive species. University of Cambridge, Corpus Christi College, Cambridge CB2 3EJ, UK [hln33@cam.ac.uk], Marc Ravinet: genomics, speciation & hybridization. University Park, Nottingham, NG7 2RD, UK [Mark.Ravinet@nottingham.ac.uk], Andrew Foote: genomics, speciation, marine mammals. NTNU University Museum, Erling Skakkes gate 47B, 7012 Trondheim, NORWAY [andrew.foote@ntnu.no] No need for them to be recommenders of PCIEvolBiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2022-04-14 15:30:42

Fernando Racimo