Biology subjects

Dion-Cote, A.-M.

Publications and source records attributed to Dion-Cote, A.-M..

7 recordsLinked to original sources

bioRxiv2025

Sex-specific modifications of gametogenesis in natural and lab-bred Fundulus spp. hybrids

Successful interspecific hybridization can be limited by a variety of reproductive barriers, including the emergence of asexual lineages which, while relatively rare in animals, is an example of a strong post zygotic barrier. In vertebrates, asexual reproduction typically arises through gametogenic alterations such as premeiotic genome endoreplication or meiotic failure, yet the relative frequency of and conditions leading to these alterations remain poorly understood. Here, we investigate natural, all female clonal hybrid lineages and laboratory-bred hybrids of both sexes between two North American killifishes, the Banded Killifish (Fundulus diaphanus) and Common Killifish (F. heteroclitus), to determine the mechanisms underlying and maintaining the emergence of asexual reproduction. By combining cytogenetic, molecular, and gametogenetic analyses, we show that all natural and some lab-bred F1 hybrid females can produce diploid and tetraploid oocytes, with natural hybrids producing a higher proportion of tetraploid eggs. In diploid oocytes, we observed both bivalents and univalents. In contrast, tetraploid oocytes exclusively formed bivalents with normal crossover formation, consistent with premeiotic genome endoreplication restoring proper meiotic pairing and facilitating clonal reproduction. Wild and lab-bred hybrid males do not undergo premeiotic genome duplication and exhibit extensive chromosomal mispairing, leading to aberrant meiotic divisions, elevated apoptosis, and decreased fertility or sterility. Together, these findings highlight sex-specific differences in gametogenesis, paralleling patterns observed in other systems, and emphasize the relative ease with which asexual reproduction can arise in hybrid females, in contrast to the sterility commonly observed in hybrid males.

evolutionary biology↗

bioRxiv2025

Accumulation of a biparentally-inherited Neptune transposable element in natural Killifish hybrids (Fundulus diaphanus X F. heteroclitus)

Transposable elements (TEs) are abundant selfish genetic elements that can mobilize in their host genome, causing DNA damage, mutations and chromosome rearrangements. TE silencing is thus critical, and is initiated by maternally loaded piRNAs, leading to their repression. Consistently, paternally inherited TEs are derepressed in the progeny of Drosophila crosses involving a naive female. TEs have also been found to be derepressed in interspecific crosses, which is proposed to result from suboptimal interactions of piRNA pathway proteins. Fundulus heteroclitus and F. diaphanus hybridize in nature and produce viable and fertile offspring that sometimes reproduce asexually. We characterized the repetitive DNA content of these species and their asexually reproducing hybrids. TE load was slightly higher than expected in hybrids and associated with younger repeats. Two bi-parentally inherited active Neptune subfamilies showed a remarkable [~]3-4-fold accumulation in hybrids. These results are consistent with suboptimal piRNA pathway function, leading to active TE accumulation.

evolutionary biology↗

bioRxiv2024

Intraspecific differences in alkaline tolerance in brook stickleback (Culaea inconstans) inhabiting neutral and alkaline lakes

Exposure to alkaline water (pH > 9.0) is physiologically challenging for fish, yet our understanding of the physiology of alkaline tolerance in fishes is limited to a small number of ihighly specialized species. This study aimed to characterize mechanisms of alkaline tolerance in brook stickleback (Culaea inconstans), a fish species with a broad pH habitat range, including highly alkaline waters such as Buffalo Lake (pH = 9.2) in Alberta, Canada. Stickleback from Buffalo Lake and a neutral reference lake (Buck Lake; pH = 8.2) were collected from the wild and acclimated to common conditions (pH = 8.0) for at least 2 months. Both populations were then exposed to alkaline conditions (pH = 9.5), resulting in a significant decrease in survival (14% by 7 d of exposure) in Buck Lake fish, but no mortality in Buffalo Lake stickleback. In a 4-d exposure to alkaline water, fish from both populations experienced characteristic inhibitions of ammonia excretion followed by subsequent recovery, in conjunction with an accumulation of ammonia within the body. However, no differences were observed between populations. Analysis of tissue Na+ and Cl- content showed a more pronounced decrease in Cl- in Buck Lake fish, suggesting that tighter regulation of Cl- homeostasis and/or acid-base balance may be an important feature of alkaline tolerance. RNA-sequencing analysis highlighted large differences in gene expression between the alkaline and neutral lake populations, and in response to alkaline exposure. Few of these changes in the expression involved genes known to be associated with nitrogen, ion, or acid-base balance. These data indicate that alkaline tolerance is higher in brook stickleback resident to an alkaline lake than those sourced from a neutral lake, a trait that may be related to differences in physiological and transcriptomic responses to alkaline exposure.

physiology↗

bioRxiv2023

Haplotype independence contributes to evolvability in the long-term absence of sex in a mite

Some unique asexual species persist over time and contradict the consensus that sex is a prerequisite for long-term evolutionary survival. How they escape the dead-end fate remains enigmatic. Here, we generated a haplotype-resolved genome assembly based on a single individual and collected genomic data from worldwide populations of the parthenogenetic diploid oribatid mite Platynothrus peltifer to identify signatures of persistence without sex. We found that haplotypes diverge independently since the transition to asexuality at least 20 my ago. Multiple lines of evidence indicate disparate evolutionary trajectories between haplotypic blocks. Our findings imply that such haplotypic independence can lead to non-canonical routes of evolvability, helping some species to adapt, diversify and persist for millions of years in the absence of sex. One-Sentence SummaryFunctionally different chromosome sets in an asexual mite species showcase a survival strategy spanning millions of years.

evolutionary biology↗

bioRxiv2023

Testing a candidate meiotic drive locus identified by pool sequencing

Meiotic drive biases the transmission of alleles in heterozygous individuals, such that Mendels law of equal segregation is violated. Most examples of meiotic drive have been discovered over the past century based on causing sex-ratio distortion or the biased transmission of easily scoreable genetic markers that were linked to drive alleles. More recently, several approaches have been developed that attempt to identify distortions of Mendelian segregation genome-wide. Here we test a candidate female meiotic drive locus in Drosophila melanogaster, identified previously as causing a [~]54:46 distortion ratio using sequencing of large pools of backcross progeny. We inserted fluorescent visible markers near the candidate locus and scored transmission in thousands of individual progeny. We observed a small but significant deviation from the Mendelian expectation, however it was in the opposite direction to that predicted based on the original experiments. We discuss several possible causes of the discrepancy between the two approaches, noting that subtle viability effects are particularly challenging to disentangle from potential small-effect meiotic drive loci. We conclude that pool sequencing approaches remain a powerful method to identify candidate meiotic drive loci, but that genotyping of individual progeny at early developmental stages may be required for robust confirmation.

genetics↗

bioRxiv2019

Rapid evolution at the telomere: transposable element dynamics at an intrinsically unstable locus

Drosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85 D. melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we suggest instead that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than a third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes with niche specialization and telomere instability being previously underappreciated and likely predominant.

genetics↗

bioRxiv2018

Programmed DNA elimination of germline development genes in songbirds

Genomes can vary within individual organisms. Programmed DNA elimination leads to dramatic changes in genome organisation during the germline-soma differentiation of ciliates1, lampreys2, nematodes3,4, and various other eukaryotes5. A particularly remarkable example of tissue-specific genome differentiation is the germline-restricted chromosome (GRC) in the zebra finch which is consistently absent from somatic cells6. Although the zebra finch is an important animal model system7, molecular evidence from its large GRC (>150 megabases) is limited to a short intergenic region8 and a single mRNA9. Here, we combined cytogenetic, genomic, transcriptomic, and proteomic evidence to resolve the evolutionary origin and functional significance of the GRC. First, by generating tissue-specific de-novo linked-read genome assemblies and re-sequencing two additional germline and soma samples, we found that the GRC contains at least 115 genes which are paralogous to single-copy genes on 18 autosomes and the Z chromosome. We detected an amplification of [≥]38 GRC-linked genes into high copy numbers (up to 308 copies) but, surprisingly, no enrichment of transposable elements on the GRC. Second, transcriptome and proteome data provided evidence for functional expression of GRC genes at the RNA and protein levels in testes and ovaries. Interestingly, the GRC is enriched for genes with highly expressed orthologs in chicken gonads and gene ontologies involved in female gonad development. Third, we detected evolutionary strata of GRC-linked genes. Developmental genes such as bicc1 and trim71 have resided on the GRC for tens of millions of years, whereas dozens have become GRC-linked very recently. The GRC is thus likely widespread in songbirds (half of all bird species) and its rapid evolution may have contributed to their diversification. Together, our results demonstrate a highly dynamic evolutionary history of the songbird GRC leading to dramatic germline-soma genome differences as a novel mechanism to minimise genetic conflict between germline and soma.

evolutionary biology↗