Distinguishing contemporary hybridization from past introgression with post-genomic ancestry-informative SNPs in strongly differentiatedCionaspecies

Abstract

One important outcome of biological introductions is to bring into contact species that diverged in allopatry. For interfertile taxa, the evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. In this context, the recent secondary contact between the non-native species Ciona robusta and the native species C.intestinalis, in the English Channel, provides an excellent case study to examine. By means of a population genomic approach, using 310 SNPs developed from full transcriptomes, the genetic diversity at population and species level was examined by studying 449 individuals (NC.robusta = 213, NC. intestinalis = 236) sampled in 12 sites from the English Channel, North Sea, NW Atlantic and SE Pacific where they are found either alone or living in the same locality and habitat (syntopy). As expected from previous analyses, C. robusta showed less polymorphism than C. intestinalis, a pattern that may partly be explained by its non-native status in most of the study localities. The results clearly showed an almost complete absence of contemporary gene flow between the two species in syntopic localities, with only one first generation hybrid and none other genotype compatible with recent backcrosses. Interestingly, introgression was also observed in allopatric populations of both species (i.e. where no contemporary hybridization can occur). Furthermore, one allopatric population sampled in SE Pacific exhibited a much higher introgression rate compared to all others C. robusta populations. Altogether, these results indicate that the observed inter-specific gene flow is the outcome of historical introgression, spread afterward at a worldwide scale. They also point out that efficient barriers are preventing hybridization in the wild between the introduced and native species in the English Channel, thus making adaptive introgression of the introduced species unlikely to favor the sustainable establishment of the study non-native species.

Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate

“…While we found here no direct evidence that intraspecific hybridization influences colonization, our results indicate that this may be a possible mechanism promoting successful colonization of sites with new environmental conditions, such as trans‐oceanic introductions. This builds on a growing number of studies showing that the mixing of divergent genotypes as a result of human mediated transport of species has the potential to fundamentally alter colonization patterns and to unprecedentedly alter ecological and evolutionary patterns (Bouchemousse, Liautard‐Haag, et al, ; Mooney & Cleland, ; Pineda, López‐Legentil, & Turon, ).…”

“…This propensity to foul can lead to negative economic and ecological impacts when this species is found in aquaculture facilities (Fitridge et al, ; Lutz‐Collins, Ramsay, Quijón, & Davidson, ; Rius et al, ). Consequently, most research studying the extensive distribution of C. intestinalis has been performed considering individuals found on artificial structures (e.g., Bouchemousse, Bishop, et al, ; Bouchemousse, Liautard‐Haag, Bierne, & Viard, ; Hudson et al, ; Zhan, Macisaac, & Cristescu, ). This has led to a good understanding of the distribution of C. intestinalis on artificial structures, but there is still limited knowledge of the relative importance of natural and artificial habitats for the spread and establishment of this species in new areas.…”

Cryptic and extensive hybridization between ancient lineages of American crows

“…We compared genomic hybrid indices to intertaxon heterozygosities to determine whether individual crows were recent‐generation hybrids or descendants of long‐admixed populations (Bouchemousse et al, 2016; Milne & Abbott, 2008). We designated crows as parental American or parental Northwestern if these respective ancestry proportions exceeded 0.98 in our combined K = 2 Bayesian clustering runs (Scordato et al, 2017).…”

“…Comparing widths of mtDNA and nuDNA clines can elucidate additional speciation mechanisms, such as the presence of sex‐biased asymmetries in dispersal or the effects of Haldane's rule (Toews & Brelsford, 2012). The relative age of a hybrid zone can also be inferred because the heterozygosity of admixed individuals decreases with each generation of backcrossing (Bouchemousse, Liautard‐Haag, Bierne, & Viard, 2016; Milne & Abbott, 2008). In addition, the presence of pronounced peaks of differentiation across the genome may indicate elevated selection within certain genomic regions, possibly related to the evolution of morphologically cryptic reproductive isolating mechanisms.…”

Temporal correlation of population composition and environmental variables in the marine invader Ciona robusta

“…The two invasive Ciona species, namely C. intestinalis ( C. intestinalis type B) and C. robusta ( C. intestinalis type A), show complex global genetic patterns (Bouchemousse, Bishop, & Viard, ) and are sympatric in the Western English Channel, where the absence of recent hybridization signature points to the presence of strong reproductive barriers (Bouchemousse, Liautard‐Haag, Bierne, & Viard, ; Caputi et al, ). The first records of C. robusta in the Mediterranean basin date to the second half of the 19th century (reviewed in Hoshino & Nishikawa, ).…”