Biology subjects

Bafort, Q.

Publications and source records attributed to Bafort, Q..

7 recordsLinked to original sources

bioRxiv2026

Highly repeatable phenotypic consequences of whole genome duplication in Spirodela polyrhiza

Whole-genome duplication (WGD) is widespread in plants, yet the extent to which it yields predictable phenotypic outcomes remains unclear. Here we show that the phenotypic consequences of genome doubling in a duckweed model system, Spirodela polyrhiza, are highly repeatable and largely deterministic. We previously generated three independent colchicine-induced autotetraploids from each of nine globally distributed diploid genotypes and, here, quantified growth and morphology across a salt gradient. In benign conditions, diploids grew faster, whereas tetraploids had larger, thicker fronds; with increasing salinity, the diploid advantage diminished and tetraploids often matched or exceeded diploid growth. Variance partitioning revealed that ploidy per se explains more phenotypic variation, including salt tolerance, than genotypic background, with rare within-genotype stochasticity. These results indicate that the shifts in morphology and stress tolerance from genome doubling are predictable and can outweigh the phenotypic effect from genetic sequence diversity.

evolutionary biology↗

bioRxiv2024

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

SummaryO_LIWhole genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. C_LIO_LIChlamydomonas reinhardtii, a haploid green alga, is a valuable model organism with profound potential to study the impact of ploidy increase on the longer-term in a laboratory environment. This is partly due to the ability to successfully increase the ploidy level. C_LIO_LIWe developed a strategy to engineer ploidy in Chlamydomonas reinhardtii using a collection of non-interfering antibiotic selectable markers. This approach allows to induce higher ploidy levels in Chlamydomonas reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy. C_LIO_LIWe demonstrate the creation of diploids, triploids and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in Chlamydomonas reinhardtii. C_LIO_LIOur study greatly facilitates the application of Chlamydomonas reinhardtii to study polyploidy, both in fundamental and applied settings. C_LI

synthetic biology↗

bioRxiv2024

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Genome merging is a common phenomenon in many organisms, causing a wide range of consequences on phenotype, adaptation, and gene expression, among other effects, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. In this study, we employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection (LNS) experiment. Utilizing fitness assays, qPCR, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution over time. Our findings reveal substantial alterations in gene expression, protein homeostasis (proteostasis) and cytonuclear stoichiometry. Notably, gene expression exhibited expression level dominance and transgressivity (i.e., expression level higher or lower than either parent). Ongoing expression level dominance and a pattern of "functional dominance" from the haploid parent was observed, alongside remarkable stability in expression patterns across generations. Despite major nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.

evolutionary biology↗

bioRxiv2023

Interspecific transfer of genetic information through polyploid bridges

Many organisms have more than two sets of chromosomes, due to whole genome duplication (WGD), and are thus polyploid. Despite usually being an ephemeral state in the history of life, polyploidy is widely recognized as an important source of genetic novelty over macroevolutionary scales. More recently, polyploidy has also been shown to facilitate interspecific gene flow, circumventing reproductive barriers between their diploid ancestors. Yet, the implications of WGD-linked introgression on community-level evolutionary dynamics remain unknown. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of viability, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents WGD-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, which allows a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with non-zero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on evolutionary change within and between mixed-ploidy populations.

evolutionary biology↗

bioRxiv2023

Non-indigenous seaweeds in the Northeast Atlantic Ocean, the Mediterranean Sea and Macaronesia: a critical synthesis of diversity, spatial and temporal patterns

Effective monitoring and combatting the effect of non-indigenous seaweeds relies on a solid confirmation of the non-indigenous status of the species. We critically analysed the status of presumed non-indigenous seaweed species reported from the Mediterranean Sea, the Northeast Atlantic Ocean and Macaronesia, resulting in a list of 140 species whose non-indigenous nature is undisputed. For an additional 87 species it is unclear if they are native or non-indigenous (cryptogenic species) or their identity requires confirmation (data deficient species). We discuss the factors underlying both taxonomic and biogeographic uncertainties and outline recommendations to reduce uncertainty about the non-indigenous status of seaweeds. Our dataset consisted of over 19,000 distribution records, half of which can be attributed to only five species (Sargassum muticum, Bonnemaisonia hamifera, Asparagopsis armata, Caulerpa cylindracea and Colpomenia peregrina), while 56 species (40%) are recorded no more than once or twice. In addition, our analyses revealed considerable variation in the diversity of non-indigenous species between the geographic regions. The Eastern Mediterranean Sea is home to the largest fraction of non-indigenous seaweed species, the majority of which have a Red Sea or Indo-Pacific origin and have entered the Mediterranean Sea mostly via the Suez Canal. Non-indigenous seaweeds with native ranges situated in the Northwest Pacific make up a large fraction of the total in the Western Mediterranean Sea, Lusitania and Northern Europe, followed by non-indigenous species with a presumed Australasian origin. Uncertainty remains, however, regarding the native range of a substantial fraction of non-indigenous seaweeds in the study area. In so far as analyses of first detections can serve as a proxy for the introduction rate of non-indigenous seaweeds, these do not reveal a decrease in the introduction rate, indicating that the current measures and policies are insufficient to battle the introduction and spread of non-indigenous species in the study area. HighlightsO_LINon-indigenous seaweed species in the Northeast Atlantic Ocean, the Mediterranean Sea and Macaronesia are critically reanalysed. C_LIO_LI>19,000 distribution records revealed considerable variation in diversity of non-indigenous seaweed species in the study area. C_LIO_LITaxonomic and biogeographic uncertainties hamper a critical evaluation of the non-indigenous status of many seaweed species. C_LI

plant biology↗

bioRxiv2023

The duplication of genomes and gene regulatory networks and its potential for evolutionary adaptation and survival

The importance of whole genome duplication (WGD), or polyploidy, for evolution, is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that (the establishment of) polyploidy can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive non-polyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short - or even immediate - term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs - and thus duplicated genomes - show higher signal output variation than non-duplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide new insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.

evolutionary biology↗

bioRxiv2017

The importance and adaptive value of life history evolution for metapopulation dynamics

O_LIThe spatial configuration and size of patches influence metapopulation dynamics by altering colonisation-extinction dynamics and local density-dependency. This spatial forcing as determined by the metapopulation typology then imposes strong selection pressures on life history traits, which will in turn feedback on the ecological metapopulation dynamics. Given the relevance of metapopulation persistence for biological conservation, and the potential rescuing role of evolution, a firm understanding of the relevance of these eco-evolutionary processes is essential.\nC_LIO_LIWe here follow a systems modelling approach to quantify the importance of spatial forcing and experimentally observed life history evolution for metapopulation demography as quantified by (meta)population size and variability. We therefore developed an individual based model matching an earlier experimental evolution with spider mites to perform virtual translocation and invasion experiments that would have been otherwise impossible to conduct.\nC_LIO_LIWe show that (1) metapopulation demography is more affected by spatial forcing than by life history evolution, but that life history evolution contributes substantially to changes in local and especially metapopulation-level population sizes, (2) extinction rates are minimised by evolution in classical metapopulations, and (3) evolution is optimising individual performance in metapopulations when considering the importance of more cryptic stress resistance evolution.\nC_LIO_LIEcological systems modelling opens up a promising avenue to quantify the importance of eco-evolutionary feedbacks for larger-scale population dynamics. Metapopulation sizes are especially impacted by evolution but its variability is mainly determined by the spatial forcing.\nC_LIO_LIEco-evolutionary dynamics can increase the persistence of classical metapopulations. The maintenance of evolutionary dynamics in spatially structured populations is thus not only essential in the face of environmental change; it also generates feedbacks that impact metapopulation persistence.\nC_LI\n\nData-archiveMetadata population dynamics in artificial metapopulations data are available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.18r5f (De Roissart, Wang & Bonte 2015). Modeling code is available on: https://github.ugent.be/pages/dbonte/eco_evo-metapop/ (ODD protocol in supplementary material)

evolutionary biology↗