Biology subjects

Fields, P. D.

Publications and source records attributed to Fields, P. D..

18 recordsLinked to original sources

bioRxiv2026

Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies

Daphnia magna is a widely used model organism in ecological genomics, ecotoxicology, and evolutionary biology. While a few genome assemblies of this species of freshwater crustacean are available, disagreements in their chromosomal arrangements point toward scaffolding problems. We present the most contiguous chromosome-level genome assembly of D. magna, the first based on PacBio HiFi sequencing technology. The assembly spans 184.38 Mb and has a scaffold N50 of 12.4 Mb. Eight of ten chromosomal scaffolds consist of mainly two contigs, representing one chromosome arm each. Eleven of 20 telomeric regions are fully resolved. Using a genomic map and comparative genomics, we were able to not only resolve the problems of previous assemblies, but also to demonstrate that some of the scaffolding errors followed a systematic pattern, most likely resulting from mis-joins during Hi-C scaffolding. Additionally, we provide expression profiles for annotated genes derived from different D. magna RNA-seq datasets, enabling rapid assessment of predicted gene expression and identification of potential pseudogenes. The new genomic and transcriptomic resource enables comparative genomic studies on genome architecture, structural variation, and gene family evolution in this important model organism.

genomics↗

bioRxiv2025

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

Genomic language models (gLMs) have emerged as a powerful approach for learning genome-wide functional constraints directly from DNA sequences. However, standard gLMs adapted from natural language processing often require extremely large model sizes and computational resources, yet still fall short of classical evolutionary models in predictive tasks. Here, we introduce GPN-Star (Genomic Pretrained Network with Species Tree and Alignment Representation), a biologically grounded gLM featuring a phylogeny-aware architecture that leverages whole-genome alignments and species trees to model evolutionary relationships explicitly. Trained on alignments spanning vertebrate, mammalian, and primate evolutionary timescales, GPN-Star achieves state-of-the-art performance across a wide range of variant effect prediction tasks in both coding and non-coding regions of the human genome. Analyses across timescales reveal task-dependent advantages of modeling more recent versus deeper evolution. To demonstrate its potential to advance human genetics, we show that GPN-Star substantially outperforms prior methods in prioritizing pathogenic and fine-mapped GWAS variants; yields unprecedented enrichments of complex trait heritability; and improves power in rare variant association testing. Extending beyond humans, we train GPN-Star for five model organisms - Mus musculus, Gallus gallus, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana - demonstrating the robustness and generalizability of the framework. Taken together, these results position GPN-Star as a scalable, powerful, and flexible new tool for genome interpretation, well suited to leverage the growing abundance of comparative genomics data.

bioinformatics↗

bioRxiv2025

Accessible, realistic genome simulation with selection using stdpopsim

Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting selection and to explore theoretical predictions. stdpopsim is a community-maintained simulation library that already provides an extensive catalog of species-specific population genetic models. Here we present a major extension to the stdpopsim framework that enables simulation of various modes of selection, including background selection, selective sweeps, and arbitrary distributions of fitness effects (DFE) acting on annotated subsets of the genome (for instance, exons). This extension maintains stdpopsims core principles of reproducibility and accessibility while adding support for species-specific genomic annotations and published DFE estimates. We demonstrate the utility of this framework by comparing methods for demographic inference, DFE estimation, and selective sweep detection across several species and scenarios. Our results demonstrate the robustness of demographic inference methods to selection on linked sites, reveal the sensitivity of DFE-inference methods to model assumptions, and show how genomic features, like recombination rate and functional sequence density, influence power to detect selective sweeps. This extension to stdpopsim provides a powerful new resource for the population genetics community to explore the interplay between selection and other evolutionary forces in a reproducible, user-friendly framework.

evolutionary biology↗

bioRxiv2025

Variation in genome architecture and epigenetic modification across the microsporidia phylogeny

Microsporidia are a model clade for studying intracellular parasitism, being well-known for their streamlined genomes and their extreme life history. Although microsporidia are highly diverse and ecologically important to a broad range of hosts, previous research on genome architecture has focused primarily on the mammal-infecting genus Encephalitozoon. Here, we expand that work, testing the universality of the patterns observed in Encephalitozoon by investigating and comparing variation in genetic and epigenetic architectures in the high-quality genome assemblies of several major microsporidia clades. Our comparison of nine genomes, including the first genome assemblies of Binucleata daphniae, Gurleya vavrai, and Conglomerata obtusa, and revised, improved assemblies of Glugoides intestinalis and Ordospora colligata, found limited conservation of genetic and epigenetic architecture across all microsporidia, although many genomic characteristics, such as nucleotide composition and repeat content, were shared between genomes of the same or related clades. For example, rRNA genes were hypermethylated in all species, but their position close to chromosome ends was only found in the Encephalitozoon and its sister clade. GC-content varied widely, linked to genome size, phylogenetic position and activity of repeat elements. These findings enhance our insight into genome evolution and, consistent with findings from other systems, suggest epigenetic modification as a regulatory mechanism of gene expression and repeat element activity in microsporidia. Our comparative genome analysis reveals higher variation among microsporidia than previously supposed.

evolutionary biology↗

bioRxiv2024

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex in a Planktonic Crustacean

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as homologs. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class. SignificanceUnderstanding how organisms adapt to their environment requires insights into the evolution of genetic defenses against their parasites. While the Major Histocompatibility Complex (MHC) is a well-known example of a highly variable immune-related gene region, much remains unknown about the evolution of other such regions. Our study investigates the Pasteuria Resistance Complex (PRC) in water fleas, a genomic region crucial for defense against a parasitic bacterium. We discovered that the PRC is exceptionally diverse, with a history spanning hundreds of millions of years. This research provides new insights into the mechanisms underlying the maintenance of genetic diversity in the face of persistent parasite pressure. Our findings contribute to a broader understanding of how organisms evolve robust defenses against infectious diseases.

evolutionary biology↗

bioRxiv2024

Trehalose mediates salinity-stress tolerance in a crustacean

Salinization poses an increasing problem worldwide, threatening freshwater organisms and raising questions about ability to adapt. We explore the mechanisms enabling a planktonic crustacean to tolerate elevated salinity. By gradually raising water salinity in clonal cultures from 185 Daphnia magna populations, we showed that salt tolerance strongly correlates with native habitat salinity, indicating local adaptation. A GWAS revealed a major effect of the Alpha,alpha-trehalose-phosphate synthase (TPS) gene, suggesting that trehalose production facilitates salinity tolerance. We found a positive correlation between water salinity and trehalose concentrations in tolerant animals, while intolerant animals failed to produce trehalose. Using CRISPR/Cas9, a silenced TPS gene supported the role of trehalose under salt stress. Our study highlights how a keystone freshwater animal adapts to salinity stress using an evolutionarily conserved mechanism known in plants and bacteria, but not in metabolic-active animals. HighlightsO_LISalinity tolerance is a locally adapted trait in Daphnia magna C_LIO_LIThe trehalose TPS gene shows a strong association with salinity tolerance C_LIO_LITrehalose content increases with water salinity allowing survival of tolerant genotypes C_LIO_LINon-functional TPS genes reduce salinity tolerance by preventing trehalose production C_LI

evolutionary biology↗

bioRxiv2024

The genome of Pasteuria ramosa reveals a high turnover rate of collagen-like genes

Collagen-like proteins (CLP) are commonly found in many pathogenic bacteria where they serve as adhesins to attach to host tissue. The repetition of the amino-acid pattern (Gly-Xaa-Yaa)n is the major feature of collagen and is essential to the formation of its stable triple helical structure. In the Daphnia magna-Pasteuria ramosa system, a model system for studying antagonistic coevolution, a specific CLP in the virulent parasite P. ramosa plays a pivotal role in host attachment, regulated by matching allele model. Recognizing the crucial role of CLPs in the infection process, we aimed to enhance our understanding of P. ramosa-CLPs by sequencing high-quality genomes of two isolates, using long-read technology. An analysis of a CLP gene tree of representative Bacillota species revealed a clear radiation of these genes in P. ramosa, which was not found in the closely related Pasteuria penetrans. A comparison of the isolates reveals a high synteny, with the exception of a few duplications and inversions, mainly involving CLPs or transposases. Across isolates, we observed a recent burst of transposases as well as duplications of CLP genes. On average, CLP genes are well conserved between isolates, but the presence/absence of individual CLP genes is not fully shared, with 39 and 43 genes in the two isolates. Our findings suggest a rapid radiation of CLP genes combined with a birth and death process of the large P. ramosa-CLP gene family, possibly driven by transposition and coevolution. ImportanceAlthough the host-pathogen Daphnia magna-Pasteuria ramosa system has served as a model for coevolution, we have, to date, lacked high-quality genomic resources for the parasite, as is the case for many such systems. By presenting a complete assembly of two distinct P. ramosa isolates, our study addresses this lack and provides deeper insights into the P. ramosa Collagen Like Protein (CLP) family, essential proteins involved in attachment to the host. We discover that the rapid radiation of CLP genes in P. ramosa appears to be driven by transposition and coevolution, enabling the parasite to adapt to host resistance mechanisms. These insights improve our understanding of host-parasite interactions and pave the way for comparative genomic analyses to better understand the evolution of these genes. They also have broader implications for disease control and therapeutic development targeting pathogenic bacteria adhesion mechanisms.

genomics↗

bioRxiv2024

Genome-wide allele frequency changes reveal that dynamic metapopulations evolve differently

BackgroundTwo important characteristics of metapopulations are extinction- (re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in "classical" (large, stable, panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation-selection-drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum (SFS). ResultsWe followed changes in SFS distribution in a natural metapopulation of the cyclically parthenogenetic pond-dwelling microcrustacean Daphnia magna using biannual pool-seq samples collected over a five-year period from 118 ponds occupied by subpopulations of known age. As expected under the propagule model, SFSs in newly founded subpopulations trended toward intermediate allele frequencies and shifted toward right skewed distributions as the populations aged. Immigration and subsequent hybrid vigor altered this dynamic. ConclusionsThe analysis of SFS dynamics is a powerful approach to understand evolution in metapopulations. It allowed us to disentangle evolutionary processes occurring in a natural metapopulation, where many subpopulations evolve in parallel. Thereby, stochastic processes like founder and immigration events lead to a pattern of subpopulation divergence, while genetic drift, leads to converging SFS distributions in the persisting subpopulations. The observed processes are well explained by the propagule model and highlight that metapopulations evolve differently from classical populations.

evolutionary biology↗

bioRxiv2023

The Silene latifolia genome and its giant Y chromosome

In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant [~]550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a [~]11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence SummaryThis work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia, which is almost 10 times larger than the human Y, despite similar genome sizes.

genomics↗

bioRxiv2023

Chromosome-level genome assembly for the angiosperm Silene conica

The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on PacBio HiFi, Hi-C and Bionano technologies. The assembly produced 10 scaffolds (one per chromosome) with a total length of 862 Mb and only [~]1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genuss ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes. SignificanceWhole-genome sequences have been largely lacking for species in the genus Silene even though these flowering plants have been used for studying ecology, evolution, and genetics for over a century. Here, we address this gap by providing a high-quality nuclear genome assembly for S. conica, a species known to have greatly accelerated rates of sequence and structural divergence in its mitochondrial and plastid genomes. This resource will be valuable in understanding the coevolutionary interactions between nuclear and cytoplasmic genomes and in comparative analyses across this highly diverse genus.

genomics↗

bioRxiv2023

Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis

Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents a first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences, and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56 % interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism. SignificanceMicrosporidia are a model for genome evolution in response to intracellular parasitism, but we lack high-quality resources from species with large genomes. We present a near complete assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis, and obtain high-quality gene annotations through full-length transcripts using Iso-Seq, a novel approach in microsporidia. Our study provides insights into gene regulation and paves the way for comparative genomic analyses aiming to understand the evolution of genome reduction and expansion in these intracellular parasites.

genomics↗

bioRxiv2022

Single-molecule sequencing of animal mitochondrial genomes reveals chloroplast-like architecture and repeat-mediated recombination

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of mitochondrial genome architecture and landscapes of recombination. We used PacBio sequencing to re-assemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a [~]1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by assembly of short sequencing reads and likely corresponding to a large non-coding region commonly present in mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy region (LSC) and a small single-copy region (SSC) separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of "flip-flop" recombination, apparently mediated by the IRs. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive inter-molecular recombination between SNPs in the LSC region. Together, these observations suggest that mitochondrial inheritance is not strictly maternal in these snails. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of such architecture, whether and how recombination mediates mitochondrial genome evolution, and the role of genome architecture in driving cytoplasmic genome biology and the maintenance of cytoplasmic genomes.

evolutionary biology↗

bioRxiv2022

Genetic drift shapes the evolution of a highly dynamic metapopulation

The dynamics of extinction and (re)colonization in habitat patches are common features of metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared to the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in more isolated, younger subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that the evolutionary process is largely driven by genetic drift.

evolutionary biology↗

bioRxiv2022

Population genetic analysis reveals the role of natural selection and phylogeography on genome-wide diversity in an extremely compact and reduced microsporidian genome

The determinants of variation in a species genome-wide nucleotide diversity include historical, environmental, and stochastic aspects. This diversity can inform us about the species past and present evolutionary dynamics. In parasites, the mode of transmission and the interactions with the host might supersede the effects of these aspects in shaping parasite genomic diversity. We used genomic samples from ten populations of the microsporidian parasite Ordospora colligata to investigate present genomic diversity and how it was shaped by evolutionary processes, specifically, the role of phylogeography, co-phylogeography (with the host), natural selection, and transmission mode. Although very closely related microsporidia cause diseases in humans, O. colligata is specific to the freshwater crustacean Daphnia magna and has one of the smallest known eukaryotic genomes. We found an overlapping phylogeography between O. colligata and its host highlighting the long-term, intimate relationship between them. The observed geographic distribution reflects previous findings that O. colligata exhibits adaptations to colder habitats, which differentiates it from other microsporidian gut parasites of D. magna predominantly found in warmer areas. The co-phylogeography allowed us to calibrate the O. colligata phylogeny and thus estimate its mutation rate. We found patterns of more efficient purifying selection in O. colligata relative to other microsporidia sharing the same host, which likely allowed this parasite to maintain its very compact genome. We also identified regions under potential selection related to coevolution including the ribosomal protein L24, a leucyl-tRNA synthetase, and a putative ABC-like lipid transport protein. Our whole-genome study provides insights into the evolution of one of the most reduced eukaryotic genomes and shows how different processes shape genomic diversity of an obligate parasite. Author summaryMicrosporidia are intracellular parasites that infect vertebrates, invertebrates, and even unicellular organisms. Due to their high variation in many aspects of life history and genomics, microsporidia have become a model clade for understanding evolutionary processes related to intracellular parasitism. However, the evolution of extreme genomic architectures in microsporidia and the coevolution with their hosts is still under-surveyed, especially given their role in human disease. Here, we study past and present evolutionary dynamics in a microsporidian species with one of the smallest known eukaryotic genomes, O. colligata. Close relatives of O. colligata cause death and disease in humans and agriculturally important animals. We show that purifying selection helped maintaining its reduced, compact genome and corroborate hypotheses about the evolution of different genome sizes in microsporidia. Importantly, we utilize the highly resolved phylogeny of its host to estimate the parasites mutation rate. This methodology allowed us to establish the first mutation rate estimate for a microsporidium, an estimate which is within the range of mutation rates estimated for phylogenetically related, non-parasitic fungi. Our study exemplifies how the combined knowledge about a species biology, ecology, and genomic diversity helps to resolve its evolutionary dynamics, in particular when phylogenomic information can be brought to bear for both host and parasite.

evolutionary biology↗

bioRxiv2022

A genomic analysis of parasite-mediated population differentiation in a metapopulation

Understanding the genetics of host adaptation is a powerful approach to study host - parasite interactions. Hosts are often assumed to have a simple genetic architecture underlying resistance. However, in natural populations the genetics are rarely known and the link between host adaptation and evolutionary models cannot be easily established. To shed light on the genetic basis of host evolution in the presence and absence of parasites we studied a highly dynamic rockpool metapopulation of the planktonic crustacean Daphnia magna and its microsporidian parasite Hamiltosporidium tvaerminnensis. We examined genome-wide allele frequencies estimated from pooled Illumina sequencing (Pool-seq) of 12 subpopulations of a metapopulation. Subpopulations that had evolved for several years with the parasite were contrasted to uninfected subpopulations, with the aim to find genomic sites of diversifying selection. Consistent with earlier attempts to find resistance genes in this system, we observe many minor-effect outliers, suggesting that the response of the host to this parasite is based on a quantitative-trait architecture. We found 34 outliers across 11 genomic regions that indicate increased differentiation between population groups as well as signs of positive selection. Some of these regions contain immune-related genes, of which four are likely involved in immune downregulation. Our findings show that in the presence of the microsporidium parasite, hosts evolve in a complex polygenic way, driving population differentiation in the metapopulation under study. Such evolutionary differentiation is a powerful mechanism to maintain genetic diversity in spatially structured populations.

evolutionary biology↗

bioRxiv2022

Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome

Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent datasets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641-kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations. Significance statementNuclear genomes are riddled with insertions of mitochondrial DNA. The model plant Arabidopsis has one of largest of these insertions ever identified, which at over 600-kb in size represents one of the last unresolved regions in the Arabidopsis genome more than 20 years after the insertion was first identified. This study reports the complete sequence of this region, providing insights into the origins and subsequent evolution of the mitochondrial DNA insertion and a resource for distinguishing between the actual mitochondrial genome and this nuclear copy in functional studies.

genomics↗

bioRxiv2021

Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution

Analyzing variation in a species genomic diversity can provide insights into its historical demography, biogeography and population structure, and thus, its ecology and evolution. Although such studies are rarely undertaken for parasites, they can be highly revealing because of the parasites coevolutionary relationships with hosts. Modes of reproduction and transmission are thought to be strong determinants of genomic diversity for parasites and vary widely among microsporidia (fungal-related intracellular parasites), which are known to have high intraspecific genetic diversity and interspecific variation in genome architecture. Here we explore genomic variation in the microsporidium Hamiltosporidium, a parasite of the freshwater crustacean Daphnia magna, looking especially at which factors contribute to nucleotide variation. Genomic samples from 18 Eurasian populations and a new, long-read based reference genome were used to determine the roles that reproduction mode, transmission mode and geography play in determining population structure and demographic history. We demonstrate two main H. tvaerminnensis lineages and a pattern of isolation-by-distance, but note an absence of congruence between these two parasite lineages and the two Eurasian host lineages. We suggest a comparatively recent parasite spread through Northern Eurasian host populations after a change from vertical to mixed-mode transmission and the loss of sexual reproduction. While gaining knowledge about the ecology and evolution of this focal parasite, we also identify common features that shape variation in genomic diversity for many parasites, e.g., distinct modes of reproduction and the intertwining of host-parasite demographies.

evolutionary biology↗

bioRxiv2020

Population history and the differential consequences of inbreeding and outcrossing in a plant metapoplation

The phenotypic consequences of inbreeding typically result in a fitness decline proportional to the increase in the inbreeding coefficient, F. This basic assumption of a predictable, inverse relationship between fitness and F has been questioned by a number of empirical studies. We explored the relationship between population history and inbreeding in a metapopulation of the plant Silene latifolia, for which long-term data are available for the historical size and spatial distribution of hundreds of local demes. We used a population genetic analysis to estimate gene flow and bi-parental inbreeding (FIS) in demes with different histories of spatial isolation. A controlled crossing experiment examined whether the effect of inbreeding and outcrossing on fitness-related traits varied with different histories of population size and isolation. Historically isolated demes experienced less gene flow and an increase in FIS, as well as significant inbreeding advantage and outbreeding depression for traits expressed early in life. The causes of variation in the F-fitness relationship among populations will include variance in the distribution of deleterious recessive alleles driven by aspects of population history, including population size, founder effects, gene flow, bi-parental inbreeding, and opportunities for the purging of genetic load. Our findings show that isolation and historical variation in population size likely contribute substantial variation in past inbreeding and the consequences of future inbreeding across the metapopulation.

evolutionary biology↗