Biology subjects

Oomen, R. A.

Publications and source records attributed to Oomen, R. A..

7 recordsLinked to original sources

bioRxiv2025

Chromosomal inversions assist acute salinity and temperature adaptation in Atlantic cod (Gadus Morhua) eggs

Chromosomal inversions, on chromosomes 2, 7, and 12 in Atlantic cod (Gadus morhua), have been consistently associated with environmental gradients, particularly salinity and temperature, across the species natural range. While these correlations suggest a role for local adaptation, the underlying selective mechanisms remain unresolved. Critically, few experiments have yet tested the fitness consequences of these inversions under controlled environmental conditions. Such work is essential to establish causality. Here, we conducted an acute stressor experiment with ten treatments of combined temperature and low salinity stress. Cod eggs (N = 1265) were placed into each treatment for 24 hours, and the number of individuals that floated initially and finally was counted. The ability of an egg to float is directly related to its survival, as sunk individuals cannot survive, and individuals lose buoyancy after they die. Inversion genotypes for the inversions on chromosomes 2, 7, and 12 were determined for individuals from the T03-S25, T07-S25, T16-S25, and T16-S35 treatments. We found that sinking increased with temperature and that more individuals sank in 25 ppt than in 35 ppt after 24 hours. Interestingly, some individuals in the 25 ppt treatments recovered (sank initially but floated finally) after 24 hours. We found evidence that the inversions on chromosomes 2 and 12 might assist with temperature and salinity adaptation, respectively, in cod eggs, while the inversion on chromosome 7 did not affect floating. Our results can inform the management and conservation of this endangered species. Summary statementWe show that chromosomal inversions found in Atlantic cod help with adaptation to short-term temperature and salinity stress at the egg stage.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the most extreme environments where flowering plants can thrive and the speciation mechanisms of plants dwelling on high alpine sky islands. The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 413 Mb, composed of 253 contigs and 101 scaffolds, with contig and scaffold N50 values of 4.95 Mb and 21.2 Mb, respectively.

genomics↗

bioRxiv2023

Contextualising samples: Supporting reference genomes for European biodiversity through sample and associated metadata collection

The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europes eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGAs pan- European network. To demonstrate the communitys capability and capacity to realise ERGAs ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGAs member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGAs high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

genomics↗

bioRxiv2022

Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data

ObjectiveAs sequencing technologies become more accessible and bioinformatic tools improve, genomic resources are increasingly available for non-model species. Using a draft genome to guide transcriptome assembly from RNA sequencing data, rather than performing assembly de novo, affects downstream analyses. Yet, direct comparisons of these approaches are rare. Here, we compare the results of the standard de novo assembly pipeline ( Trinity) and two reference genome-based pipelines ( Tuxedo and the new Tuxedo) for differential expression and gene ontology enrichment analysis of a companion study on Atlantic cod (Gadus morhua). ResultsThe new Tuxedo pipeline produced a higher quality assembly than the Tuxedo suite. However, greater enrichment of Trinity-identified differentially expressed genes suggests that a higher proportion of them represent biologically meaningful differences in transcription, as opposed to transcriptional noise or false positives. Coupled with the ability to annotate novel loci, the increased sensitivity of the Trinity pipeline might make it preferable over the reference genome-based approaches for studies aimed at broadly characterizing variation in the magnitude of expression differences and biological processes. However, the new Tuxedo pipeline might be appropriate when a more conservative approach is warranted, such as for the identification of candidate genes.

bioinformatics↗

bioRxiv2021

Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures

Although temperature is known to drive species dynamics and distributions, our understanding of the extent to which thermal plasticity varies within species is poor. Differences in plasticity can arise through local adaptation to heterogeneous environments, hybridization, and the release of cryptic genetic variation in novel environments. Here, wild Atlantic cod (Gadus morhua) from contrasting environments inside and outside of a fjord system in southern Norway spawned freely in a semi-natural laboratory environment, generating pure crosses and reciprocal hybrids. A common-garden rearing experiment of the larvae at 6{degrees}C, 9.5{degrees}C, and 13{degrees}C revealed cryptic genetic variation in thermal responses of growth and survival at warmer temperatures. Variation in growth plasticity was greatest from 9.5{degrees}C to 13{degrees}C, the latter of which exceeds temperatures currently typical of larvae in their native environments. In contrast to our prediction of intermediate hybrid responses consistent with additive genetic effects, one reciprocal hybrid cross showed a 4% increase in size at the highest temperature, whereas most crosses exhibited 4-12% reductions in size. All crosses experienced severe (76-93%) reductions in survival from 9.5{degrees}C to 13{degrees}C. Variation in survival plasticity suggests a genetically variable basis for the severity with which survival declines with increasing temperature and the potential for an adaptive response to warming. Notably, we demonstrate the potential for hybridization between coexisting fjord and North Sea ecotypes that naturally inhabit the inner and outer fjord environments at contrasting frequencies. Yet, ecotype explained a minor (3-10%) component of growth reaction norm variation, suggesting it is insufficient for describing important biological variation. Current broad-scale management and lack of coastal monitoring impede the development of strategies to maintain the potential for adaptation to warming temperatures in systems with such phenotypic complexity resulting from cryptic genetic variation, coexisting ecotypes, and gene flow.

evolutionary biology↗

bioRxiv2020

Changes in group size during resource shifts reveal drivers of sociality across the tree of life

From biofilms to whale pods, organisms have repeatedly converged on sociality as a strategy to improve individual fitness. Yet, it remains challenging to identify the most important drivers--and by extension, the evolutionary mechanisms--of sociality for particular species. Here, we present a conceptual framework, literature review, and model demonstrating that the direction and magnitude of the response of group size to sudden resource shifts provides a strong indication of the underlying drivers of sociality. We catalog six functionally distinct mechanisms related to the acquisition of resources, and we model these mechanisms effects on the survival of individuals foraging in groups. We find that whether, and to what degree, optimal group size increases, decreases, or remains constant when resource abundance declines depends strongly on the dominant mechanism. Existing empirical data support our model predictions, and we demonstrate how our framework can be used to predict the dominant social benefit for particular species. Together, our framework and results show that a single easily measurable characteristic, namely, group size under different resource abundances, can illuminate the potential drivers of sociality across the tree of life.

animal behavior and cognition↗

bioRxiv2020

Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change

Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modelling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multi-locus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.

evolutionary biology↗