Biology subjects

Bartos, O.

Publications and source records attributed to Bartos, O..

7 recordsLinked to original sources

bioRxiv2026

Rapid evolution of cone identity and retinal topography in deep-water crater lake cichlids

Deep-water habitats have been colonized repeatedly by fishes, driving the evolution of visual systems under extremely low-light conditions. Here, we investigated visual adaptation in cichlids from the Barombi Mbo crater lake by comparing shallow- and deep-water species using retinal single-cell transcriptomics and analyses of retinal specializations. The shallow-water species Pungu maclareni expressed a broader repertoire of visual opsins across distinct populations of short- (SWS), medium- (RH2), and long-wavelength-sensitive (LWS) cone photoreceptors. In contrast, the deep-water species Myaka myaka lacked a distinct LWS cone population and instead relied predominantly on RH2A/{beta}-expressing, green-sensitive photoreceptors. To assess whether these deep-water RH2 cones corresponded to canonical RH2 or LWS programmes, we compared conserved photoreceptor markers. Deep-water RH2 cones retained elements of both RH2- and LWS-associated transcriptional programmes, revealing a mixed profile lacking a clear canonical cone-type signature. LWS-associated transcriptional regulators also differed between species, with tbx2a absent from M. myaka cones, consistent with the loss of LWS opsin expression, whereas thrb persisted in M. myaka RH2 cones. We further examined retinal specialization across eight species from the radiation and found that retinal topography also differed in photoreceptor distributions and ganglion cell-based acuity centers in association with habitat depth but also with trophic ecology of the species. Together, our findings show that visual adaptation in a young adaptive radiation involves coordinated changes in visual opsin expression, cone-associated transcriptional programmes, and retinal organization, highlighting how sensory systems can quickly evolve through changes at multiple biological levels in response to ecological conditions.

evolutionary biology↗

bioRxiv2025

Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis

It has been empirically established that genome mixing between divergent species can trigger meiotic aberrations, ultimately leading to the emergence of asexual reproduction through the production of unreduced gametes in various metazoan lineages. Yet, it remains poorly understood how such asexual hybrids cope with co-inherited differences in sex determination systems, diverged regulatory networks, and chromosomal incompatibilities-- especially in the context of increased ploidy. Addressing these questions requires high-quality, chromosome-level reference genomes of the parental species involved in hybrid formation. Here, we present the first chromosome-level genome assemblies for three hybridizing Cobitis species (C. elongatoides, C. taenia, and C. tanaitica), providing a comprehensive framework to investigate the genetic and cytogenetic basis of hybrid sterility and the transition to asexuality. By integrating genome scaffolding, male/female pooled sequencing, and molecular cytogenetics, we uncover extensive structural variation among homologous chromosomes of the three species, despite their overall syntenic conservation. Population-level Pool-Seq analyses further revealed that each species possesses a distinct, non-homologous sex chromosome, highlighting sex chromosome turnover even among recently diverged lineages. These assemblies enabled the design of chromosome-specific painting probes, which we applied to meiotic metaphase I spreads of diploid hybrids. This approach revealed striking differences in the pairing success of orthologous chromosomes, with some (e.g., Ch01B) frequently forming bivalents, while others (e.g., Ch01A, Ch05, Ch20) failed to do so and remained unpaired. Our results demonstrate that chromosome-specific features, shaped by structural evolution and sex-linked divergence, contribute unequally to hybrid meiotic failure. Together, this work provides a high-resolution genomic and cytogenetic framework to understand how interspecific hybridization gives rise to clonality, and how the architecture of inherited parental genomes shapes the success or breakdown of meiosis in hybrid vertebrates.

genomics↗

bioRxiv2025

Seeing in the deep: evolution of the opsin gene expression in Bermin crater lake cichlids

Cichlid visual systems can evolve rapidly during adaptive radiations. This study investigates the Bermin crater lake species flock in Cameroon, comprising thirteen (nine valid and four undescribed) Coptodon species, to explore the effects of deep-water light environments on visual evolution. We analyzed visual opsin genes and their expression using 109 retina transcriptomes, focusing on differences among species at varying depths, and seasonal changes in the visual system of a seasonally migrating species. All species exhibit a multichromatic system with at least five cone opsins. While opsin sequence variability among species was minimal due to the flocks evolutionary youth, opsin expression patterns varied significantly. Deep-water species showed reduced SWS1 and SWS2B expression, consistent with diminished UV-to-violet light in deeper waters. Unexpectedly, we observed increased proportional expression of the red-sensitive LWS opsin gene, contrary to trends seen in other lacustrine fishes. Additionally, in the seasonally deep-dwelling species Coptodon imbriferna, opsin expression varied plastically between the rainy (shallow) and dry (deep) seasons, with reduced SWS2B expression when the fish reside in the deeper habitats. To add context of other cichlid systems and to explore shared patterns of molecular adaptation, we compared Bermin cichlids to the deep-water species of the Barombi Mbo crater lake. Both cases exemplify independent evolution of deep-water species, yet their visual systems adapted similarly in the single cones (less UV- and violet-sensitive and more blue-sensitive cones), whereas differently in the long-wavelength sensitive double cones (LWS expression lost in Barombi while increased in Bermin). Overall, our study focuses on an evolutionarily young example of cichlid adaptive radiation, providing a unique opportunity to examine the initial phases of molecular adaptation in visual systems.

evolutionary biology↗

bioRxiv2024

Hemoglobin gene repertoire in teleost and cichlid fishes shaped by gene duplications and genome rearrangements

Hemoglobin is a crucial element of the oxygen transport system in vertebrates. It exhibits remarkable gene diversity across teleost fishes, reflecting their evolutionary adaptations for thriving in various aquatic environments. In this study, we present the dynamic evolution of hemoglobin subunit genes based on a comparison of high quality long-read genome assemblies of 24 vertebrate species, including 16 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain between five (fugu) and 43 (salmon) hemoglobin genes, representing the largest hemoglobin gene repertoire among vertebrates. We find evidence that the ancestor of teleosts had at least four Hb and three or four Hb{beta} subunit genes, and that the current gene diversity emerged during subsequent teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organization of hemoglobin clusters, revealing the parallel origin of multiple clusters in tetrapods and in teleosts. Importantly, we show that the presence of paralogous rhbdf1 genes flanking both teleost hemoglobin clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environments has been shown to play roles in species diversification. Our analysis of six cichlid genomes, including the Pungu maclareni from crater lake Barombi Mbo, for which we sequenced the representative genome, reveals 18 to 31 copies of the Hb genes, and elevated rates of non- synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how hemoglobin genes contribute to the adaptive and diversification potential of teleosts.

evolutionary biology↗

bioRxiv2023

Genetic and karyotype divergence between parents affect clonality and sterility in hybrids

Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad phylogenetic spectrum, assessed by whole exome data. Gametogenic pathways generally followed a continuum from sexual reproduction in hybrids between closely related evolutionary lineages to sterile or inviable crosses between distant lineages. However, most crosses resulted in a combination of sterile males and asexually-reproducing females. Their gametes usually experienced problems in chromosome pairing, but females also produced a certain proportion of oocytes with premeiotically duplicated genomes, enabling their development into clonal eggs. Interspecific hybridization may thus commonly affect cell cycles in a specific way, allowing the formation of unreduced oocytes. The emergence of asexual gametogenesis appears tightly linked to hybrid sterility and constitutes an inherent part of the extended speciation continuum.

evolutionary biology↗

bioRxiv2022

Revealing genomic changes responsible for cannabinoid receptor loss in parrots: mechanism and functional effects

In vertebrates, an ancient duplication in the genes for cannabinoid receptors (CNRs) allowed the evolution of specialised endocannabinoid receptors expressed in the brain (CNR1) and the periphery (CNR2). While dominantly conserved throughout vertebrate phylogeny, our comparative genomic analysis suggests that certain taxa may have lost either the CNR1 regulator of neural processes or, more frequently, the CNR2 involved in immune regulation. Focussing on conspicuous CNR2 pseudogenization in parrots (Psittaciformes), a diversified crown lineage of cognitively-advanced birds, we highlight possible functional effects of such a loss. Parrots appear to have lost the CNR2 gene at at least two separate occasions due to chromosomal rearrangement. Using gene expression data from the brain and periphery of birds with experimentally-induced sterile inflammation, we compare CNR and inflammatory marker (interleukin 1 beta, IL1B) expression patterns in CNR2-deficient parrots (represented by the budgerigar, Melopsittacus undulatus and five other parrot species) with CNR2-intact passerines (represented by the zebra finch, Taeniopygia guttata). Though no significant changes in CNR expression were observed in either parrots or passerines during inflammation of the brain or periphery, we detected a significant up-regulation of IL1B expression in the brain after stimulation with lipopolysaccharide (LPS) only in parrots. As our analysis failed to show evidence for selection on altered CNR1 functionality in parrots, compared to other birds, CNR1 is unlikely to be involved in compensation for CNR2 loss in modulation of the neuroimmune interaction. Thus, our results provide evidence for the functional importance of CNR2 pseudogenization for regulation of neuroinflammation.

genomics↗

bioRxiv2020

Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection and link to gene function

AbstractHybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. During their evolution, the subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that may enforce specific evolutionary pathways. We studied the genome evolution in asexual diploid and polyploid hybrids between fish from the genus Cobitis. Comparing exome sequencing with published cytogenetic and RNAseq data revealed that clonal genomes remain static on chromosome-scale levels but undergo considerable small-scale restructurations owing to two major processes; hemizygous deletions and gene conversions. Interestingly, polyploids were much more tolerant to accumulating deletions than diploid asexuals where gene conversions prevailed. The genomic restructurations accumulated preferentially in genes characterized by high transcription levels, relatively strong purifying selection and some specific functions such as interacting with intracellular membranes. The likelihood of an orthologs retention or loss correlated with its parental-species ancestry, GC content, and expression. Furthermore, all hybrids showed a strong bias towards the retention of one parental subgenome. Contrary to expectations, however, the preferentially retained subgenome was not transcriptionally dominant as all hybrids were phenotypically more similar to the other parent. The present study demonstrated that the fate of subgenomes in asexual hybrids and polyploids depends on the complex interplay of selection and several molecular mechanisms whose impact depends on ploidy, sequence composition, gene expression as well as parental ancestry.

evolutionary biology↗