Biology subjects

Oosterhout, C. v.

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

4 recordsLinked to original sources

bioRxiv2026

The genomic basis of evolutionary stasis in the 500-million-year-old red seaweed genus Ahnfeltia

The red seaweed genus Ahnfeltia is an ancient lineage that has persisted for over 500 million years with remarkably limited diversification despite a global distribution in cold-temperate intertidal habitats. Compared to the highly diverse sister lineage, Rhodymeniophycidae, Ahnfeltia provides a unique system for investigating long-term evolutionary persistence in marine macroalgae. Here, we generated chromosome-scale genomes from five populations across three species and combined population genomics with paleogeographic niche modelling. Our results reveal remarkable genomic conservation, strong geographic isolation with limited gene flow, high homozygosity, and evidence of purifying selection. Niche projections indicate long-term stability and spatial connectivity of suitable cold-temperate habitats. These findings suggest that Ahnfeltias persistence and limited diversification are linked to genomic constraints and stable ecological niches over geological timescales. This study provides new insights into the genomic basis of evolutionary stasis in ancient marine lineages and highlights potential vulnerability to ongoing climate change affecting cold-water coastal ecosystems.

evolutionary biology↗

bioRxiv2026

Selection mode governs the scaling of genetic load, diversity, and adaptation

Nearly neutral theory predicts that deleterious alleles can behave approximately neutrally when selection is weak relative to genetic drift. For codominant mutations, the conventional nearly neutral threshold is |s| {approx} 1/(2Ne); thus, when Ne = 500, a mutation with |s| = 0.001 lies at this threshold. For strongly recessive mutations, however, newly arisen copies occur mainly in heterozygotes, so selection is much weaker while they are rare. We used forward-time simulations to test whether competitive soft selection can purge strongly recessive deleterious mutations that behave as nearly neutral under hard selection. The focal mutations had s = -0.001 and h = 0.01, placing their effect when rare about 50-fold below the corresponding nearly neutral threshold. Under hard selection, these mutations behaved almost neutrally, continuing to accumulate, with some reaching fixation. Under rank-based soft selection, accumulation was strongly suppressed; at high fecundity, mutations remained at low frequency and none reached fixation. Purging strengthened as more candidates competed for a fixed number of recruitment opportunities. A pairwise tournament produced the same qualitative but slightly weaker pattern. Thus, competitive soft selection can purge rare, recessive deleterious mutations whose effects fall well below the nearly neutral threshold under hard selection. By acting on aggregate multilocus fitness differences, relative competition may reduce genetic load and susceptibility to inbreeding depression. These findings are also relevant to genic capture, whereby many weak effects of deleterious mutations contribute to genome-wide genetic quality that can be exposed through competition and sexual selection.

evolutionary biology↗

bioRxiv2022

Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. This could result in the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of Spike gene (S). The 5' genome portion (circa 22 kb) resembles the AY.101 lineage (VOC Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 lineage (VOC Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, named AYBA-RS, is one out of almost 30 recombinants described this year. The submission of only four sequences in the GISAID database suggests that this Brazilian lineage had a minor epidemiological impact. On the other hand, the recent emergence of this and various other Deltacron recombinant lineages (i.e., XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that support this assertion, and we conclude that this stresses the need for continued genomic and epidemiological surveillance. This is particularly important for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.

evolutionary biology↗

bioRxiv2021

Evolutionary epidemiology of a zoonosis

Cryptosporidium parvum is a global zoonoses and a major cause of diarrhoea in humans and ruminants. The parasites life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and all are likely recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalisation and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race. Data SummaryAll raw and processed sequencing data generated and analysed during the current study have been submitted to the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject/), under BioProjects PRJNA634014 and PRJNA633764.

evolutionary biology↗