Biology subjects

van Oosterhout, C.

Publications and source records attributed to van Oosterhout, C..

18 recordsLinked to original sources

bioRxiv2026

Inbreeding depression and population viability in a recovering population of Mauritius kestrels

Inbreeding depression (the reduction in fitness associated with inbreeding) has been demonstrated in a wide range of animals, but despite its ubiquity, is not an inevitable consequence of inbreeding. As a result, there is uncertainty about the extent to which inbreeding depression poses an ongoing risk to endangered species currently experiencing significant demographic recovery. Quantifying inbreeding depression will be critical if we want to understand these risks. A comprehensive quantification of the fitness costs of inbreeding requires detailed individual-based longitudinal data so lifetime impacts can be assessed. Here, we use an extraordinarily detailed long-term dataset on Mauritius kestrels (Falco punctatus) to explore inbreeding depression in a population currently experiencing significant demographic recovery. To do so, we constructed a social pedigree of 1,758 individuals and combined this with 1,240 nest records and 1,411 individual resighting histories to explore lifetime fitness effects over a 30-year period. Inbreeding increased significantly over time as the population recovered before stabilising. Inbred eggs were less likely to survive to fledging. Inbred adult male and female birds had significantly lower annual reproductive success than outbred individuals because of a lower annual egg-to-fledgling survival probability. This resulted in significantly lower lifetime reproductive success in inbred females but not males, which showed a negative trend. Population growth was negative and extinction risk increased slightly at current levels of inbreeding. These impacts will become more severe should inbreeding levels increase in the future, which is highly likely given ongoing genomic erosion. Taken together, our results demonstrate significant fitness costs associated with inbreeding in Mauritius kestrels, which pose an ongoing risk to population viability. This suggests that monitoring and managing inbreeding risks in endangered species will likely be required even in populations that are showing significant demographic recovery in response to conservation interventions.

ecology↗

bioRxiv2026

Conservation rescued the Mauritius kestrel from extinction but not from genomic erosion

Conservation can prevent species extinction via demographic recovery, yet it remains debated whether this translates into genomic recovery and restored fitness. The Mauritius kestrel (Falco punctatus) declined to four known wild birds in 1974 before intensive management recovered the population. Using 130 genomes spanning nearly 200 years, lifetime reproductive success data, and simulations, we reconstructed genomic change across the species collapse and recovery. Long-term small population size had already removed some harmful variation before the crash, a process expected to buffer populations from severe inbreeding depression. Yet the recent bottleneck sharply increased inbreeding, exposed additional harmful variants, and left a signature of genomic erosion associated with reduced reproductive success. The long conservation history of the Mauritius kestrel shows how population collapse and recovery can leave a compounding genetic threat, in which partial genetic purging, continuing genomic erosion, and conservation dependence unfold together in rescued species.

evolutionary biology↗

bioRxiv2026

An introgressed galectin-like protein is a candidate driver of the human tropism in the intestinal parasite Cryptosporidium

Cryptosporidium spp. are protozoan parasites responsible for diarrheal diseases. In humans, cryptosporidiosis is predominantly caused by the human-specific Cryptosporidium hominis and by Cryptosporidium parvum. This second species has been classically reported as zoonotic, with a host preference for ruminants. However, the recently described subspecies C. parvum anthroponosum has been found to be restricted to humans. Here, we generated novel whole genome sequences from West African samples of C. p. anthroponosum, and analyzed them together with all those already available, originating from East Africa, Europe, North America and Asia. Phylogenomics showed that all C. p. anthroponosum isolates are strongly clustered together, forming the sister clade of the zoonotic C. parvum representatives. The phylogenetic variations within C. p. anthroponosum did not present a clear geographic structure, consistent with C. hominis, primarily transmitted in humans. To elucidate the evolution of host species adaptation in C. p. anthroponosum, we then investigated genetic exchanges with C. hominis, detecting an ancestral introgression present in all C. p. anthroponosum isolates. This introgression involved a single gene, encoding for an extracellular galectin-like protein, which we predicted with high confidence to form a protein complex with the human insulin-degrading enzyme, a key metabolic regulator. Considering the role of host insulin metabolism in the proliferation of parasites as well as its known intrinsic differences between humans and ruminants, this molecular interaction could represent a plausible mechanism for an important role of the galectin-like protein in host-parasite interactions and in the host specificity of C. p. anthroponosum.

genomics↗

bioRxiv2025

Genomic erosion through the lens of comparative genomics

Loss of genetic diversity threatens species survival, yet the dynamics of such loss and species responses thereof can vary widely depending on their evolutionary histories, life-history traits and demographic trajectories. Comparative genomics offers a powerful framework to explore the dynamics of genomic erosion across species. Here, we analysed the genomes of three species -- the Mauritius parakeet, the Mauritius kestrel, and the pink pigeon -- that experienced extreme and well-documented population bottlenecks. We compared them to 36 species spanning the avian phylogeny, with varied IUCN Red List statuses to investigate the genomic consequences of their demographic collapses. For each species, we assessed nucleotide diversity, genetic load, and runs of homozygosity (ROH), alongside genome synteny and transposable elements. We found a negative correlation between nucleotide diversity and ROH, but neither metric was a good predictor of the species Red List status. Rather, the population effective to census size ratio showed a strong correlation to Red List status. Moreover, species with larger historical effective population sizes showed greater heterozygosity but carried a higher heterozygous load, highlighting the importance of historical demography to assess species vulnerability to genomic erosion. We found significant differences in homozygous load between taxonomic groups of our target species, possibly due to differences in life-history traits and demographic histories. Genome structure analyses revealed differences in transposable elements and genomic rearrangements between groups, suggesting their potential role in shaping genome architecture and adaptive potential across species. Our findings underscore the value of multispecies comparisons in understanding the evolutionary dynamics of genomic erosion and its relevance for biodiversity conservation.

genomics↗

bioRxiv2024

Persistent genomic erosion in whooping cranes despite demographic recovery

Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating into a collapse to 16 individuals in 1941. Legal protections and conservation actions have since increased the population to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality genome reference, and re-sequencing 16 historical and 37 modern genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its genetic diversity and has increased their inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realized load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and background inbreeding argues against the species downlisting from their current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realized load. Our findings emphasize the role of genomics in informing conservation management and policy.

evolutionary biology↗

bioRxiv2024

Calculating and interpreting FST in the genomics era

The relative genetic distance between populations is commonly measured using the fixation index (FST). Traditionally inferred from allele frequency differences, the question arises how FST can be estimated and interpreted when analysing genomic datasets with low sample sizes. Here, we advocate an elegant solution first put forward by Hudson et al. (1992): FST = (Dxy -{pi} xy)/Dxy, where Dxy and{pi} xy denote mean sequence dissimilarity between and within populations, respectively. This multi-locus FST-metric can be derived from allele frequency data, but also from sequence alignment data alone, even when sample sizes are low and/or unequal. As with other FST-metrices, the numerator denotes net divergence (Da), which is equivalent to the f2-statistic and Neis D (for realistic estimates of Dxy and{pi} xy). In terms of demographic inference, net divergence measures the difference in increase of Dxy and{pi} xy since the population split, owing to a reduction of coalescence times within populations as a result of genetic drift. Because different combinations of{Delta} Dxy and{Delta}{pi} xy can produce identical FST-estimates, no universal relationship exists between FST and population split time. Still, in case of recent population splits, when novel mutations are negligible, FST-estimates can be accurately converted into coalescent units ({tau}. i.e., split time in multiples of 2Ne). This then allows to quantify gene tree discordance, without the need for multispecies coalescent based analyses, using the formula: Pdiscordance = [2/3]{middle dot}(1 - FST). To facilitate the use of the Hudson FST-metric, we implemented new utilities in the R package SambaR.

genomics↗

bioRxiv2023

The ghost of selection past: evolution and conservation relevance of the kakapo color polymorphism

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living k[a]k[a]p[o] to understand the evolution of its remarkable feather color polymorphism. The k[a]k[a]p[o] is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the k[a]k[a]p[o] a "ghost of selection past".

genomics↗

bioRxiv2022

Extensive immune receptor repertoire diversity in disease-resistant rice landraces

Plants have powerful defence mechanisms, and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in south-west China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties of indica, japonica and aus using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasises the value of standing genetic variation that is maintained in farmer landraces as resource to make modern crops and agroecosystems less prone to disease.

evolutionary biology↗

bioRxiv2022

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

Fragilariopsis cylindrus CCMP1102 is characterised by a complex genome with significant levels of heterozygosity between haplotypes, > 35% repeats, and an unknown karyotype. This complexity hindered prior assemblies, which show coverage discrepancies indicative of incompleteness. Here, we use a k-mer spectra analysis to reveal the coverage signature for a third haplotype. We applied a novel haplotype-specific assembly method to reconstruct the F. cylindrus CCMP1102 genome, producing 10 fully assembled chromosomes capped by telomeres, and a putative chromosome with a single breakpoint. Our analysis shows triploidy, two cases of aneuploidy, and several truncations. We also present evidence that F. cylindrus reproduces sexually. Taken together, our analytical approach is capable of haplotype-resolved assemblies from structurally complex, poly-ploid genomes, making it suitable for complex genomes of non-model organisms, including those with unknown karyotype.

genomics↗

bioRxiv2021

VIVID: a web application for variant interpretation and visualisation in multidimensional analyses

Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3-dimensional (3D) visualisation of genotypic information encoded in Variant Call Format (VCF) on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritising targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.

bioinformatics↗

bioRxiv2021

Means, motive, and opportunity for biological invasions: genetic introgression in a fungal pathogen

Invasions by fungal plant pathogens pose a significant threat to the health of agriculture ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses in crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen on soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2 to 30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "The Means, Motive, and Opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographic areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

evolutionary biology↗

bioRxiv2021

Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution

Cryptosporidiosis is a major global health problem and a primary cause of diarrhoea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic C. hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes (GIPVs), including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a coevolutionary arms race with the host. Lastly, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, may be driving evolution of more virulent C. hominis variants.

genomics↗

bioRxiv2021

Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida

Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a non-photosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms revealed that a combination of genes loss, the horizontal acquisition of genes involved in organic carbon degradation, a unique secretome and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a non-parasitic, free-living secondary heterotroph.

genomics↗

bioRxiv2020

Mitotic interhomolog recombination drives genomic diversity in diatoms

Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific variability in natural populations. However, the process generating such diversity is unknown. Here we estimated the variability within a natural diatom population and subsequently mapped the genomic changes arising within cultures clonally propagated from single diatom cells. We demonstrate that genome rearrangements and mitotic recombination between homologous chromosomes underlie clonal variability, resulting in haplotype diversity accompanied by the appearance of novel protein variants and loss of heterozygosity resulting in the fixation of alleles. The frequency of interhomolog mitotic recombination exceeds 4 out of 100 cell divisions and increases under environmental stress. We propose that this plastic response in the interhomolog mitotic recombination rate increases the evolutionary potential of diatoms, contributing to their ecological success. One Sentence SummaryRecombination between homologous chromosomes in diatom vegetative cells leads to extensive genomic diversity in clonal populations.

genomics↗

bioRxiv2020

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) have high levels of chromosome conservation. Whether this truly reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids - an important group of hemipteran plant pests - using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published chromosome-scale assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. persicae and A. pisum) and Aphidini (R. maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-level assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny and we detect only two chromosome fusion or fission events. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.

genomics↗

bioRxiv2019

An aphid host-responsive RNA transcript that migrates systemically in plants promotes aphid reproduction

Aphids are sap-feeding insects that colonize a broad range of plant species and often cause feeding damage and transmit plant pathogens, including bacteria, viruses and viroids. These insects feed from the plant vascular tissue, predominantly the phloem. However, it remains largely unknown how aphids, and other sap-feeding insects, establish intimate long-term interactions with plants. To identify aphid virulence factors, we took advantage of the ability of the green peach aphid Myzus persicae to colonize divergent plant species. We found that a M. persicae clone of near-identical females establishes stable colonies on nine plant species of five representative plant eudicot and monocot families that span the angiosperm phylogeny. Members of the novel aphid Ya family are differentially expressed in aphids on the nine plant species, are co-regulated and organized as tandem repeats in aphid genomes. Interestingly, aphids translocate Ya transcripts into plants and some transcripts migrate systemically within several plant species. RNAi-mediated knock down of Ya genes reduces M. persicae fecundity and M. persicae produces more progeny on transgenic plants that heterologously produce one of the systemically migrating Ya transcripts as a long non-coding (lnc)RNA. Taken together, our work led to the discovery of a new host-responsive aphid gene family that operate as virulence factors. Transcripts of this family translocate into plants, including a lncRNA that migrates systemically and promotes aphid reproduction.\n\nSignificance StatementThe green peach aphid Myzus persicae causes yield losses of a diverse range of economically important crops primarily as a vector of more than 100 different plant pathogens. We found that a single genotype of M. persicae is able to colonize nine plant species, including diverse dicots and maize, indicating that this aphid is truly polyphagous. Members of a new aphid Ya family undergoes coordinated expression changes in M. persicae depending on the plant species. The aphids translocate Ya transcripts into plants during feeding and these RNAs migrate to systemic leaves. Moreover, heterologous in planta expression of M. persicae Ya1 as a long non-coding RNA promotes aphid reproduction. Our findings indicate that cross kingdom deployment of RNA is more common than thought.

genomics↗

bioRxiv2018

Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon

Early-life stress can have long-lasting effects on immunity, but the underlying molecular mechanisms are unclear. We examined the effects of acute stress (cold-shock during embryogenesis) and chronic stress (absence of tank enrichment during larval-stage) on the gill transcriptome and methylome of Atlantic salmon four months after hatching. While only chronic stress induced pronounced transcriptional effects, both acute and chronic stress caused lasting, and contrasting, changes in the methylome. Crucially, we found that acute stress enhanced immune response to a pathogenic challenge (lipopolysaccharide), while chronic stress suppressed it. We identified stress-induced changes in promoter or gene-body methylation that were associated with altered expression for a small proportion of genes, and also evidence of wider epigenetic regulation within signalling pathways involved in immune response. Our study suggests that early-life stress can affect immuno-competence through epigenetic mechanisms, a finding that could open the way for improved stress and disease management of farmed fish.

genomics↗

bioRxiv2018

Sex-specific changes in the aphid DNA methylation landscape

Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We find that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3 end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than un-methylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypo-methylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hyper-methylated. Overall, we find correlated changes in methylation and gene expression between males and asexual females, and this correlation is particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in M. persicae sexual differentiation.

genomics↗