Biology subjects

Daguin-Thiebaut, C.

Publications and source records attributed to Daguin-Thiebaut, C..

7 recordsLinked to original sources

bioRxiv2026

High gene flow in Atlantic vent shrimp species with multiple ridge colonizations by ecotypic lineages with contrasting symbioses

Conservation concerns regarding potential mineral extraction near deep-sea hydrothermal vents have emphasised the need for a better understanding of the contemporary connectivity of various vent-endemic species, accounting for the specifics of their life-history traits and habitat requirements. Rimicaris shrimps are a major component of vent communities in the Atlantic Ocean, both along the Mid-Atlantic Ridge (MAR) and at the Mid-Cayman Spreading Center (MCSC). Using ddRAD sequencing, we examined the genetic differentiation of three Atlantic Rimicaris species to better understand their past and present migration pathways and the possible demographic history that led to their current distribution and ecology. Rimicaris exoculata and R. chacei inhabit the MAR and exhibit widespread gene flow along the ridge with no areas of restricted connectivity. R. hybisae occurs at the MCSC and exhibits almost no genetic difference with its congeneric from the MAR, R. chacei, despite the geographic distance between them and their contrasting ecologies and morphologies. Demographic inferences support a scenario of a very recent (less than 2000 generations) separation between MCSC and MAR shrimp populations, followed by a rapid expansion in both regions, possibly triggered by symbiotic development. Analyses further suggest recent or ongoing secondary contacts involving two-way migration, which is more pronounced from the MCSC towards the MAR. All together these results suggest that R. chacei and R. hybisae represent distinct forms of the same species, which we hereby synonymise as R. chacei, highlighting their morphological plasticity in relation to symbiosis.

evolutionary biology↗

bioRxiv2025

Sex chromosomes and chromosomal rearrangements are key to behavioural sexual isolation in Jaera albifrons marine isopods

The lack of sexual attraction between individuals from different populations is a direct barrier to gene flow between these populations. Here we focus on the evolution of this class of isolating mechanism, behavioural sexual isolation, through the empirical study of two closely related species of small marine isopods. The males of Jaera albifrons and J. praehirsuta similarly engage females in tactile courtship by brushing a specific region of the females back, but they do so with divergent sets of specialised setae and spines, and female choice results in strong reproductive isolation. Using bi-allelic SNP genotypes obtained from double-digest RAD sequencing of individuals from natural populations and controlled crosses, we found that secondary contacts between J. albifrons and J. praehirsuta resulted in different levels of heterospecific gene flow depending on the ecological context. Comparison of the genomic landscapes of differentiation in the two most contrasting situations (extremely low heterospecific gene flow in one region of western France, but strong introgressive hybridisation in another), combined with linkage map analyses, allowed us to conclude that genomic regions resistant to interspecies gene flow are primarily located either on the sex chromosomes or on rearranged chromosomes (several fusion-scissions and one reciprocal translocation). These genomic regions show low recombination, and in two cases QTL analyses found genetic variation associated with several male courtship traits. These results suggest that a long period of allopatry may have allowed the divergent co-evolution of male traits and female preferences, with genetic bases located at least in part in non-recombining regions on sex chromosomes and rearranged chromosomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/631900v4_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@6b7df8org.highwire.dtl.DTLVardef@11b4d00org.highwire.dtl.DTLVardef@15c760aorg.highwire.dtl.DTLVardef@1498d45_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2024

Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents

How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins (BABs) of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach--especially in addressing knowledge gaps on the life history traits of deep-sea species.

evolutionary biology↗

bioRxiv2023

Genetic sex determination in three closely related hydrothermal vent gastropods, one of which has intersex individuals

Molluscs have a wide variety of sexual systems and have undergone many transitions from separate sexes to hermaphroditism or vice versa, which is of interest for studying the evolution of sex determination and differentiation. Following the serendipitous observation that sex was the primary driver of genetic structure in the hydrothermal vent gastropod Alviniconcha boucheti, we investigated sexual systems and sex determination in this species and two others of the same genus. We combined genome-wide multi-locus genotypes obtained from RAD sequencing with anatomical observations of the gonads of the three Alviniconcha species occurring in the southwest Pacific Ocean: A. boucheti (n=199), A. strummeri (n=41 ind.) and A. kojimai (n=246). In two of the species (A. boucheti and A. strummeri), the sexes are separate and genetically determined by a male-heterogametic (XY) system. External observation of the gonads in the third species (A. kojimai) also suggested that the sexes were separate, but histological analyses revealed that 76% of the individuals classified as females from external observation of the gonads presented a mosaic of male and female reproductive tissue. Empirical analyses and simulations showed nonetheless that 14 RAD loci were sex-linked with an XY signature in A. kojimai (as compared with 64 in A. strummeri and 373 in A. boucheti). Comparison across species and mapping of RAD loci to a non-contiguous reference genome assembly of the related species A. marisindica showed that all sex-linked loci identified in A. kojimai are located on five scaffolds that also contain 15 and 67 sex-linked RAD loci in the other two species, respectively. These results suggest that all three Alviniconcha species share the same XY sex determination system, but that the gonad of XX A. kojimai individuals are invaded by a variable proportion of male reproductive tissue. It remains to be seen whether the male tissue in these intersex individuals is functional or not. The identification of Y-specific RAD loci (found only in A. boucheti) and the phylogenetic analysis of three sex-linked loci shared by all species suggested that X-Y recombination has evolved differently within each species. This situation of three species showing variation in gonadal development around a probably common sex determination system provides new insights into the reproductive mode of poorly known deep-sea species and questions the evolution of gametogenetic polymorphism in these species.

evolutionary biology↗

bioRxiv2022

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

AO_SCPLOWBSTRACTC_SCPLOWHuman-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.

evolutionary biology↗

bioRxiv2021

An introgression breakthrough left by an anthropogenic contact between two ascidians

Human-driven translocations of species have diverse evolutionary consequences such as promoting hybridization between previously geographically isolated taxa. This is well-illustrated by the solitary tunicate, Ciona robusta, native to the North East Pacific and introduced in the North East Atlantic. It is now co-occurring with its congener C. intestinalis in the English Channel, and C. roulei in the Mediterranean Sea. Despite their long allopatric divergence, first and second generation crosses showed a high hybridization success between the introduced and native taxa in the laboratory. However, previous genetic studies failed to provide evidence of recent hybridization between C. robusta and C. intestinalis in the wild. Using SNPs obtained from ddRAD-sequencing of 397 individuals from 26 populations, we further explored the genome-wide population structure of the native Ciona taxa. We first confirmed results documented in previous studies, notably i) a chaotic genetic structure at regional scale, and ii) a high genetic similarity between C. roulei and C. intestinalis, which is calling for further taxonomic investigation. More importantly, and unexpectedly, we also observed a genomic hotspot of long introgressed C. robusta tracts into C. intestinalis genomes at several locations of their contact zone. Both the genomic architecture of introgression, restricted to a 1.5 Mb region of chromosome 5, and its absence in allopatric populations suggest introgression is recent and occurred after the introduction of the non-indigenous species. Overall, our study shows that anthropogenic hybridization can be effective in promoting introgression breakthroughs between species at a late stage of the speciation continuum.

evolutionary biology↗

bioRxiv2018

Sexual isolation with and without ecological isolation between sympatric isopods Jaera albifrons and J. praehirsuta

Sexual isolation is often coupled with other barriers, and sexual isolation mechanisms can be intrinsically tied to ecological conditions or natural selection against heterospecific gene flow. The independence and relative strength of sexual isolation are thus difficult to assess. Here we take advantage of a pair of isopod species (Jaera albifrons and J. praehirsuta) that show sexual isolation and coexist in populations where they share the same habitat or not (i.e. without or with ecological isolation). Using no-choice trials and a free-choice experimental population, we estimated the strength of sexual isolation between J. albifrons and J. praehirsuta individuals originating from these different ecological contexts. We found that sexual isolation is strong in presence and absence of ecological isolation, but that it is asymmetric and fails to prevent gene flow entirely. Post-zygotic barriers were low, and there was no sexual isolation within J. praehirsuta across habitats. The J. albifrons / J. praehirsuta species pair thus provides an example where the role of sexual isolation as a barrier to gene flow i) does not depend upon current ecological isolation, ii) seems to have evolved independently of local ecological conditions and hybridization costs, but iii) is unable to complete speciation entirely on its own.

evolutionary biology↗