Biology subjects

Olsen, E. M.

Publications and source records attributed to Olsen, E. M..

5 recordsLinked to original sources

bioRxiv2026

Diversity without borders: partitioning continuous spaces using probabilistic equivalent numbers

Equivalent numbers represent biodiversity as the effective number of equally distinct units, typically species, and can be partitioned across scales. In practice, they summarize each unit of biodiversity by a single value and compare units pairwise, misrepresenting units that are better described as distributions and the relationships between several units that share the same space. We introduce an equivalent-number index for assemblages of units represented as probability density functions (PDFs) over a continuous space, estimated as the integral of the pointwise maximum across abundance-weighted PDFs. Resulting equivalent PDF numbers fulfil elementary properties of classical equivalent numbers, and support additive partitioning across any number of nested scales. We illustrate the framework with case studies across three domains: (1) measuring trait diversity considering intraspecific variability in grasslands, (2) partitioning realized bioclimatic niches among clades of Carnivora, and (3) understanding seasonal changes in the partitioning of fish home ranges in geographic space.

ecology↗

bioRxiv2025

Atlantic cod (Gadus morhua) ecotypes, not inversion frequencies, underlie divergence in egg buoyancy distribution

Life-history divergence between Atlantic cod (Gadus morhua) ecotypes in Skagerrak is maintained despite gene flow. Fjord and North Sea ecotypes differ in growth, body size, and reproductive ecology. One environmental heterogeneity in Skagerrak is salinity, as coastal habitats experience substantially lower and more variable salinities than offshore waters. Egg buoyancy is highly sensitive to salinity and represents a critical life-history trait shaping survival and recruitment. Inversions on chromosomes 2, 7, and 12 in cod are linked to salinity adaptation and might be important for egg buoyancy and survival. Here, we conducted a buoyancy test on Atlantic cod eggs, spawned from North Sea and Fjord ecotypes, using Coombs apparatus. Genotypes for the inversions on chromosomes 2, 7, and 12 and ecotype were determined in all individuals (N=242). We hypothesized that individuals with different inversion genotypes and ecotypes would have divergent buoyancies. We found that buoyancy was variable and followed a bimodal distribution sorted by ecotype, with Fjord and North Sea individuals having mean buoyancies at neutral salinity (at 7{degrees}C) of 27 and 31 ppt, respectively. Therefore, individuals with intermediate buoyancies might be selected against. This finding is consistent with our expectations, as Fjord ecotypes experience lower salinities compared to North Sea ecotypes. Interestingly, there was little evidence that the inversions on chromosomes 2, 7, and 12 impacted buoyancy. Overall, we provide experimental evidence of the relative contributions of ecotypic background and inversions on a key life history trait, which helps to explain the maintained divergence among ecotypes.

evolutionary biology↗

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

Disentangling Conditional Effects of Multiple Regime Shifts on Atlantic Cod Productivity

Regime shifts are increasingly prevalent in the ecological literature. However, definitions vary, and many detection methods are subjective. Here, we employ an operationally objective means of identifying regime shifts, using a Bayesian online change-point detection algorithm able to simultaneously identify shifts in the mean and(or) variance of time series data. We detected multiple regime shifts in long-term (59-154 years) patterns of coastal Norwegian Atlantic cod (>70% decline) and putative drivers of cod productivity: North Atlantic Oscillation (NAO); sea-surface temperature; zooplankton abundance; fishing mortality (F). The consequences of an environmental or climate-related regime shift on cod productivity are accentuated when regime shifts coincide, fishing mortality is high, and populations are small. The analyses suggest that increasing F increasingly sensitized cod in the mid 1970s and late 1990s to regime shifts in NAO, zooplankton abundance, and water temperature. Our work underscores the necessity of accounting for human-induced mortality in regime shift analyses of marine ecosystems.

ecology↗