Biology subjects

Fraisse, C.

Publications and source records attributed to Fraisse, C..

9 recordsLinked to original sources

bioRxiv2023

Rapid establishment of species barriers in plants compared to animals

Speciation, the process through which new reproductively isolated species emerge from ancestral populations, occurs due to the gradual accumulation of barriers to gene flow within genomes. To date, the notion that interspecific genetic exchange occurs more frequently between plant species than animals species has gained a strong footing in the scientific discourse. By examining the dynamics of gene flow across a continuum of divergence in both kingdoms, we observe the opposite relationship: plants experience less introgression than animals at the same level of genetic divergence, suggesting that species barriers are established more rapidly in plants. This pattern raises questions about which differences in microevolutionary processes between plants and animals influence the dynamics of reproductive isolation establishment at the macroevolutionary scale. One Sentence SummaryGenetic exchange is more frequent between animal species than plants, challenging historical views.

evolutionary biology↗

bioRxiv2023

Climate change promoted allopatric divergence and explains the current disjunct geographic distribution of the Ophrys aveyronensis species complex (Orchidaceae)

AimSpecies with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful to decipher the causes of such pattern: i) actual vicariance, ii) successful colonization from one source range to a new range (dispersal, biological introduction) or iii) parallel convergent evolution. LocationSouthern France and Northern Spain. TaxonThe bee orchid Ophrys aveyronensis (and its two recognized subspecies O. a. subsp. aveyronensis and O. a. subsp. vitorica) displays a disjunct geographic distribution with two subranges separated by 600 km on both sides of the Pyrenees Mountains. MethodsThrough a combination of population genomics and Ecological Niche Modelling (ENM), we investigated the causes of this intriguing biogeographic pattern. ResultsThe population genomic data demonstrate that all the studied populations exhibit similar patterns of genetic diversity and dramatic decrease in effective size compared to the ancestral population. Significant genetic differentiation and reciprocal monophyly exist between populations of the two subranges of O. aveyronensis, despite a very recent divergence time as young as ca. 1500 generations ago. Moreover, (paleo-)ecological Niche Modelling analyses support that the disjunct geographic distribution of the O. aveyronensis is consistent with a range split of a broad ancestral range, contraction and distinct longitudinal and latitudinal shifts in response to climate warming during the Holocene. Main ConclusionThe congruence of the results obtained from both population genomics and ENM approaches documents how very recent continental allopatric divergence initiated speciation in this system. Ophrys aveyronensis provides a promising opportunity to study the onset of reproductive isolation and parallel evolution following an initial stage of geographic separation in a group with high diversification rate.

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↗

bioRxiv2020

DILS : Demographic Inferences with Linked Selection by using ABC

We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also available via a web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

evolutionary biology↗

bioRxiv2020

The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs. autosomes

Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.

evolutionary biology↗

bioRxiv2018

The distribution of epistasis on simple fitness landscapes

Fitness interactions between mutations can influence a populations evolution in many different ways. While epistatic effects are difficult to measure precisely, important information about the overall distribution is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effects sizes, mutational bias, and maladaptation of the wild-type. We illustrate our approach by reanalysing a large data set of mutant effects in a yeast snoRNA. Though characterized by some strong epistatic interactions, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have little effect on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape, and the distribution of mutations, and so it is expected to vary in consistent ways between new mutations, standing variation, and fixed mutations.

evolutionary biology↗

bioRxiv2018

Assessing the impact of high-throughput sequencing strategy and model complexity on ABC-inferred demographic history in mussels

Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

evolutionary biology↗

bioRxiv2017

Fine-grained genetic-environment association in an admixed population of mussels in the small isolated Kerguelen island

Reticulated evolution -i.e. secondary introgression / admixture between sister taxa-is increasingly recognized as a key evolutionary process that may play a role in structuring infra-specific genetic variation, and possibly promoting adaptation. Mytilus spp. is an ideal system to assess its importance, because these marine mussels form semi-isolated species that remain reproductively compatible over large time-scales. It includes three taxa that hybridize in the Northern Hemisphere (M. edulis, M. galloprovincialis and M. trossulus) and two taxa of uncertain ancestry in the Southern Hemisphere (M. platensis: South America and the Kerguelen Islands; and M. planulatus: Australasia). The Kerguelen mussels are of particular interest to investigate the potential role of admixture in enhancing micro-geographic structure, as they inhabit a small and isolated island in the Southern Ocean characterized by a highly heterogeneous environment, and genomic reticulation between Northern and Southern lineages has been suspected. Here, we extended a previous analysis by using targeted-sequencing data (51,878 SNPs) across the three Northern species and the Kerguelen population, coupled with a panel of 33 SNPs genotyped on 695 mussels across 35 sites in the Kerguelen Islands. The panel was enriched with ancestry-informative SNPs, i.e. SNPs that were more differentiated than the genomic average between Northern lineages, to evaluate whether reticulated evolution contributed to micro-geographic structure. We first showed that the Kerguelen population belongs to a divergent Southern lineage, most related to M. edulis mussels, that experienced secondary admixture with non-indigenous Northern species. We then demonstrated that the Kerguelen mussels were significantly differentiated over small spatial distance, and that this local genetic structure was associated with environmental variation and mostly revealed by ancestry-informative markers. Although local adaptation can explain the association with the environment we believe it more likely that environment variables better describe population connectivity than geographic distance. Our study highlights genetic connectivity of populations is more easily revealed by non-equilibrium secondary introgression clines at a subset of loci, while association with the environment should not be hastily advocated to support adaptation from admixture variation.

evolutionary biology↗