Biology subjects

Kivikoski, M.

Publications and source records attributed to Kivikoski, M..

5 recordsLinked to original sources

bioRxiv2025

Evolution induced state shifts in a long-term microbial community experiment

Biological communities are complex, dynamic systems that underpin ecosystem functionality1, yet their long-term dynamics and predictability remain poorly understood2. Understanding how Darwinian evolution shapes these systems through eco-evolutionary feedbacks is a central challenge in ecology and evolution. Experimental studies using simplified microbial assemblages have yielded important insights into the ecological principles governing community states3-5. However, an important knowledge gap is how selection within member species drives changes of community state in multispecies systems. Here, we present a four-year evolution experiment involving a 23-species synthetic bacterial community propagated in two environments: a control medium and the same medium supplemented with the antibiotic streptomycin. Through combined analyses of community composition and genome evolution, we quantified the temporal changes in species abundances and the evolutionary trajectories of individual community members. The extended duration of the experiment enabled the detection of adaptive mutations and community state shifts that occur only over long evolutionary timescales. We show that community dynamics are environment dependent and reproducible across replicates, and that evolution of streptomycin resistance in a previously streptomycin-sensitive species on its own can induce abrupt community state shifts. Our results provide a direct demonstration of eco-evolutionary feedbacks within a multi-species community, revealing how a single adaptive mutation can reorganize complex ecological networks.

ecology↗

bioRxiv2023

Determinants of genetic diversity in sticklebacks

Understanding what determines species and population differences in levels of genetic diversity has important implications for our understanding of evolution, as well as for the conservation and management of wild populations. Previous comparative studies have emphasized the roles of linked selection, life-history trait variation and genomic properties, rather than pure demography, as important determinants of genetic diversity. However, these findings are based on coarse estimates across a range of highly diverged taxa, and it is unclear how well they represent the processes within individual species. We assessed genome-wide genetic diversity ({pi}) in 45 nine-spined stickleback (Pungitius pungitius) populations and found that{pi} varied 15-fold among populations ({pi}min{approx}0.00015,{pi} max{approx}0.0023) whereas estimates of recent effective population sizes varied 122-fold. Analysis of inbreeding coefficients (FROH) estimated from runs of homozygosity revealed strong negative association between{pi} and FROH. Genetic diversity was also negatively correlated with mean body size and longevity, but these associations were not statistically significant after controlling for demographic effects (FROH). The results give strong support for the view that populations demographic features, rather than life history differences, are the chief determinants of genetic diversity in the wild.

evolutionary biology↗

bioRxiv2022

Low heritability of crossover rate in wild sticklebacks

Crossover rate is mostly studied with domesticated or lab-reared populations and little is known about its genetic variation in the wild. We studied the variation and genetic underpinnings of crossover rate in outbred wild nine- (Pungitius pungitius) and three-spined (Gasterosteus aculeatus) sticklebacks. In both species, the crossover rate of females exceeded that of males as did also its repeatability (RFemales =0.21-0.33, RMales=0.026-0.11), implying individual differences of crossover rate in females, but no or less so in males. However, in both species and sexes additive genetic variance and heritability of crossover rate were effectively zero. A review of the previously reported repeatability and heritability estimates revealed that the repeatabilities in stickleback females were moderately high, whereas those in males were very low. Genome-wide association analyses recovered a few candidate regions possibly involved with control of crossover rate. The low additive genetic variance of crossover rate in wild sticklebacks suggest limited evolvability of crossover rate.

evolutionary biology↗

bioRxiv2020

Effects of crossover interference on genomic recombination landscape

Map distance is one of the key measures in genetics and indicates the expected number of crossovers between two loci. Map distance is estimated from the observed recombination frequency using mapping functions, the most widely used of those, Haldane and Kosambi, being developed at the time when the number of markers was low and unobserved crossovers had a substantial effect on the recombination fractions. In contemporary high-density marker data, the probability of multiple crossovers between adjacent loci is negligible and different mapping functions yield the same result, that is, the recombination frequency between adjacent loci is equal to the map distance in Morgans. However, high-density linkage maps contain an interpretation problem: the map distance over a long interval is additive and its association with recombination frequency is not defined. Here, we demonstrate with high-density linkage maps from humans and stickleback fishes that the inverse of Haldane or Kosambi mapping functions fail to predict the recombination frequency from map distance, and show that this is because the expected number of crossovers is not sufficient to predict recombination frequency. We formulate a piecewise function to calculate the probability of no crossovers between the markers that yields more accurate predictions of recombination frequency from map distance. Our results demonstrate that the association between map distance and recombination frequency is context-dependent and no universal solution exists. We anticipate that our study will motivate further research on this subject to yield a more accurate mathematical description of map distance in the context of modern data.

genetics↗

bioRxiv2020

New gains with a slimmer genome - An automated approach to improve reference genome assemblies

We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.7 Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.

genomics↗