Biology subjects

Hodson, C. N.

Publications and source records attributed to Hodson, C. N..

10 recordsLinked to original sources

bioRxiv2026

340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera

Diptera genome evolution is traditionally viewed through the lens of Drosophila melanogaster. To provide an unbiased picture of chromosome evolution in Diptera, we reconstructed six ancestral linkage groups (ALGs) and their rearrangements using 340 chromosome-level genome assemblies from 59 dipteran Families and two outgroups. Notably, Diptera ALGs are conserved in many Nematoceran lineages, while emergence of Brachycera coincided with four chromosomal fissions, which subsequently fused in various combinations. In Schizophora and relatives, a stable karyotype of five metacentric chromosomes and a chromosome homologous to the dot emerged that is remarkably stable with the notable exception of Drosophila, where the metacentric chromosomes became acrocentric Muller elements. Furthermore, our reconstruction reveals an ancient sex chromosome system associated with a small and gene-poor ALG that frequently fused to other chromosomes.

genomics↗

bioRxiv2025

Evidence for Transcription and Horizontal Gene Transfer in Dipteran Germline-Restricted Chromosomes

Germline-restricted chromosomes (GRCs) constitute a unique class of chromosomes confined to reproductive cells. Arising across multiple evolutionarily distant lineages, GRCs have been identified in three insect families (non-biting midges, gall midges, and fungus gnats), each within the order Diptera. Genomic characterisation in fungus gnats has revealed GRCs to be large, gene-rich chromosomes, which, together with their persistence over millennia, implies they play important biological roles within this clade. However, transcription from these chromosomes has yet to be demonstrated, leaving key questions about their function and activity unresolved. Here, we provide the first direct evidence of GRC-linked gene expression in the fungus gnat Bradysia coprophila, integrating RNA-seq data with cytological observations across multiple developmental stages. We report that GRCs express functional genes, though overall transcription is highly limited, likely due to biological factors, such as transcriptional silencing in specific germline cell types, and technical constraints, including filtering to avoid mismapping from core chromosome paralogues. We identify 15 confidently expressed GRC-linked genes using stringent criteria, including five insect homologues of unknown function and nine resembling transposable elements, and report horizontal acquisition of a [~]290 kb bacterial-derived region on GRC2. Furthermore, we perform in vitro immunofluorescence staining and confocal microscopy, which indicate increased GRC activity in female oocytes. Overall, these findings establish GRCs in fungus gnats as transcriptionally active, albeit tightly regulated and highly dynamic, chromosomes capable of expressing both endogenous and potentially horizontally acquired genes.

genomics↗

bioRxiv2025

Dynamic evolution of germ-line restricted chromosomes in three dark-winged fungus gnats (Sciaridae) revealed through chromosome level germline genomes.

Germline restricted chromosomes (GRCs) are an evolutionary mystery. While they seem to be important and perhaps indispensable in species they occur, they also show surprising variability in copy number and size. We are just beginning to understand the evolutionary significance of these chromosomes. One factor that impedes our understanding is that at present, few clades with these chromosomes have been studied in depth. We genomically investigate the GRCs in dark-winged fungus gnats (Sciaridae), a cosmopolitan and species-rich taxa which have harboured GRCs for at least 58 million years. Sciaridae species carry from 1-4 large GRCs which evolved through introgression from the Cecidomyiidae lineage. We produce the first male germline chromosome-scale genome assemblies for the sciarids Bradysia coprophila, B. impatiens, and Lycoriella ingenua. Comparing the GRCs both between and within species, we find that these chromosomes evolve in an extraordinarily dynamic fashion, with very little conservation of synteny or gene content. Puzzlingly, despite this variability, GRCs are gene rich and their genes are evolving under strong purifying selection. Additionally, we uncover evidence that somatic elimination of GRCs potentially occurs via a satellite mediated process. Our study sheds light on the mechanisms of meiosis, tissue restriction, chromosome elimination, and gives us a better appreciation for the diversity of genetic systems that not only persist, but thrive in nature. Significance statementGermline restricted chromosomes (GRCs) are a fascinating evolutionary puzzle. They are restricted to the germline early in development, have unusual transmission dynamics and are more variable than core chromosomes, but also seem to be indispensable in clades they occur in. We generate chromosome level GRC assemblies from three species of fungus gnats (Sciaridae, Diptera). We find that the GRCs, which originated via a cross-family hybridization event, are evolving much more dynamically than other chromosomes in the genome. The five GRCs we sequence are all large, gene-rich, and seem to carry functional genes, but contain mostly a non-overlapping gene set, suggesting that four of the five GRCs we sequenced did not evolve from the same original chromosome.

evolutionary biology↗

bioRxiv2025

Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila

Programmed DNA elimination (PDE), a phenomenon wherein cells eliminate a subset of genetic material during certain stages of development, is observed in a broad range of organisms. The fungus gnat Bradysia (formerly Sciara) coprophila undergoes a series of PDE events during their development, including elimination of germline-restricted chromosomes (called L chromosomes) in soma and elimination of paternal chromosomes during male meiosis. However, the underlying mechanisms of this phenomenon are poorly understood. Highly repetitive satellite DNA, which often shows chromosome specific distribution, is a possible candidate for sequences involved in PDE. In this study, we utilized recent genomic data and genome assemblies to identify new satellite DNA sequences of B. coprophila. Through characterization of satellite DNA distribution on chromosomes, we found that the X and autosomes do not share centromeric satellite DNA sequence with the L chromosomes. We further provide the cytological evidence that confirms a recent finding based on the genome assembly that there are two distinct L chromosomes that were not previously distinguished cytologically. Together, our work lays a foundation for future studies to explore the possible connection between satellite DNA and the mechanism of PDE in B. coprophila.

cell biology↗

bioRxiv2024

Does non-Mendelian chromosome transmission and unusual sex determination affect male mate choice in the fly Bradysia coprophila?

Mate quality and the cost of mating affect the evolution of mating preferences and is one reason females often show stronger mate preferences than males. Fungus gnats in the family Sciaridae (Diptera) are a family in which we might expect to see the evolution of strong male mate preferences. Many Sciaridae species are monogenic, where females exclusively produce offspring of one sex. Sciaridae species also exhibit paternal genome elimination, a reproductive system where males only transmit maternally inherited chromosomes to offspring. Therefore, Sciaridae males would benefit from exhibiting mating preferences for females that produce female offspring, as a males genes are only transmitted to future generations through his daughters, not his sons. We explore male mate choice in the sciarid fly Bradysia (formerly Sciara) coprophila. We find that mating is costly, as males become sperm limited through multiple matings, and that males exhibit preferences for larger females, suggesting that males are selected to be choosy. However, we do not find male preferences for females that produce female offspring, instead we find that males prefer mating with females that produce male offspring. We speculate that this seemingly maladaptive behaviour may be due to female receptivity rather than male preference, or that males are unable to distinguish between females of different types, which is perhaps surprising since these females differ genetically by 1000s of genes (through a large paracentric inversion on the X chromosome). Together we show how the interplay between unusual genetics and sex determining systems may affect mating system evolution. Summary statementIn the fungus gnat Bradysia coprophila females are genetically predetermined to produce broods of just one sex and males only transmit maternally inherited genes to offspring. These factors suggest males should have strong mating preferences for females that produce daughters, which we explore. We find that while males would benefit from being "choosy", they appear unable to distinguish the two female types, possibly because females are selected to hide their sex determining phenotype.

evolutionary biology↗

bioRxiv2022

Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods

Sex determination is a key developmental process, yet it is remarkably variable across the tree of life. The dipteran family Sciaridae exhibits one of the most unusual sex determination systems in which mothers control offspring sex through selective elimination of paternal X chromosomes. Whereas in some members of the family females produce mixed-sex broods, others such as the dark-winged fungus gnat Bradysia coprophila are monogenic, with females producing single-sex broods. Female-producing females were previously found to be heterozygous for a large X-linked paracentric inversion (X), which is maternally inherited and absent from male-producing females. Here we assembled and characterized the X sequence. As close sequence homology between the X and X made identification of the inversion challenging, we developed a k-mer-based approach to bin genomic reads before assembly. We confirmed that the inversion spans most of the X chromosome (approximately 55Mb) and encodes around 3500 genes. Analysis of the divergence between the inversion and the homologous region of the X revealed that it originated very recently (<0.5 mya). Surprisingly, we found that the X is more complex than previously thought and is likely to have undergone multiple rearrangements that have produced regions of varying ages, resembling a supergene composed of evolutionary strata. We found functional degradation of around 7.3% of genes within the region of recombination suppression, but no evidence of accumulation of repetitive elements. Our findings provide an indication that sex-linked inversions are driving turnover of the strange sex determination system in this family of flies.

evolutionary biology↗

bioRxiv2022

Are asymmetric inheritance systems an evolutionary trap? Transitions in the mechanism of genome loss in the scale insect family Eriococcidae

Haplodiploidy and paternal genome elimination (PGE) are examples of asymmetric inheritance, where males transmit only maternally inherited chromosomes to their offspring. Under haplodiploidy this results from males being haploid, whereas under PGE males inherit but subsequently eliminate paternally inherited chromosomes during meiosis. Their evolution involves changes in the mechanisms of meiosis and sex determination, and sometimes also dosage compensation. As a result, these systems are thought to be an evolutionary trap, meaning that once asymmetric chromosome transmission evolves, it is difficult to transition back to typical Mendelian transmission. We assess whether there is evidence for this idea in the scale insect family Eriococcidae, a lineage with PGE and the only clade with a suggestion that asymmetric inheritance has transitioned back to Mendelian inheritance. We conduct a cytological survey of 13 eriococcid species, and a cytological, genetic, and gene expression analysis of species in the genus Cystococcus, to investigate whether there is evidence for species in this clade evolving Mendelian chromosome transmission. Although we find that all species we examined exhibit PGE, the mechanism is extremely variable within Eriococcidae. Within Cystococcus, in fact, we uncover a previously undiscovered type of PGE in scale insects, where in males paternally inherited chromosomes are present, uncondensed, and expressed in somatic cells, but are eliminated prior to meiosis. Broadly, we fail to find evidence for a reversion from PGE to Mendelian inheritance in Eriococcidae, supporting the idea that asymmetric inheritance systems such as PGE may be an evolutionary trap.

evolutionary biology↗

bioRxiv2021

Genomic evidence of paternal genome elimination in globular springtails

AO_SCPLOWBSTRACTC_SCPLOWPaternal genome elimination (PGE) - a type of reproduction in which males inherit but fail to pass on their fathers genome - evolved independently in six to eight arthropod clades. Thousands of species, including several important for agriculture, reproduce via this mode of reproduction. While PGE is well established in some of the clades, the evidence in globular springtails (Symphypleona) remains elusive, even though they represent the oldest and most species rich clade putatively reproducing via PGE. We sequenced genomic DNA from whole bodies of Allacma fusca males with high fractions (>27.5%) of sperm to conclusively confirm that all the sperm carry one parental haplotype only. Although it is suggestive that the single haplotype present in sperm is maternally inherited, definitive genetic proof of the parent of origin is still needed. The genomic approach we developed allows for detection of genotypic differences between germline and soma in all species with sufficiently high fraction of germline in their bodies. This opens new opportunities for scans of reproductive modes in small organisms.

genomics↗

bioRxiv2021

Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)

Germline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which carries two large germline restricted "L" chromosomes. We sequenced and assembled the genome of B. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.

evolutionary biology↗

bioRxiv2020

Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems

Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives, and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These are among the first empirical results suggesting a role for intragenomic conflict in the evolution of novel genetic systems like HD/PGE. Significance StatementSex determination systems such as haplodiploidy, in which males gene transmission is haploid, are surprisingly common, however, the evolutionary paths to these systems are poorly understood. X chromosomes may play a particularly important role, either by increasing survival of males with only maternal genomes, or due to conflicts between X-chromosomal and autosomal genes. We studied X-chromosome gene richness in three arthropod lineages in which males are diploid as adults but only transmit their maternally-inherited haploid genome. We find that species with such atypical systems have far more X chromosomal genes than related diploid species. These results suggest that conflict between genetic elements within the genome drives the evolution of unusual sex determination systems.

evolutionary biology↗