Biology subjects

Liukkonen, M.

Publications and source records attributed to Liukkonen, M..

5 recordsLinked to original sources

bioRxiv2024

Gut microbiome diversity associates with estimated lifetime and annual reproductive success in male but not female collared flycatchers

The gut microbiome (hereafter, GM) varies across individuals of the same species and this pattern has been observed in multiple wild species. Evidence shows that the GM connects to individual health and survival especially in captive species, but more research is needed to understand how the GM connects to host fitness in wild species. We used long-term monitoring data to investigate whether the GM of collared flycatchers Ficedula albicollis associates with annual and lifetime reproductive success (LRS), and survival to the following breeding season. This is the first study that 1) characterized the collared flycatcher GM, and 2) investigated how variation in the GM related to LRS in wild birds. Our results showed that higher GM diversity was associated with a higher annual and lifetime reproductive success in especially male collared flycatchers. We also found that the compositional variation in collared flycatcher GMs was explained by sex, age, and breeding habitat, but not by annual or lifetime reproductive success. Individuals that died before the next breeding season had higher abundances of ASVs belonging to the pathogenic families Enterobacteriaceae and Parachlamydiaceae, and the genera Corynebacteria and Sphingomonas. Our results show that the GM associates with different aspects of host fitness in a wild bird population. More research is needed to evaluate if there is a causal relationship between the GM and individual fitness. These findings also contribute to our understanding of the GMs role in evolution by elucidating the connection between the GM (trait) and reproductive success.

ecology↗

bioRxiv2024

Genome-wide association mapping for growth rate at fluctuating and extreme temperatures

Constant temperatures and fluctuations of varying frequency affect fitness differently, which has led to suggestions of distinct genetic architectures and adaptation strategies between constant and fluctuating thermal environments. However, very little is known about the possible fitness trade-offs and genetic constraints underlying thermal adaptation and how they affect species ability to confront climatic changes. We addressed this gap in knowledge by integrating quantitative genetics and genome-wide association mapping in the filamentous fungus Neurospora crassa. Growth rates were measured for 434 strains under fast and slow frequency fluctuations, at high and low temperature range with respect to the species tolerance, and at constant mean and extreme temperatures of these ranges. We found strong genetic correlations between fast and slow frequency fluctuations, and between fluctuations and their mean temperatures, but not with the highest extreme temperature. Positive correlations were supported by high heritability values, pointing that in N. crassa there are no significant trade-offs or genetic constraints in adaptation when variance in temperature increases. Altogether, our results indicated clearly polygenic basis of thermal tolerance, with most of the variation in overall performance (83 %), and clearly less in hot-cold trade-off (8 %), or heat stress tolerance (4 %). Interestingly, GWAS discovered many SNPs associated with growth rate only at constant temperatures or at fast and slow fluctuations at high and low thermal range. However, the cellular functions of the associated genes were overlapping, and no opposite allelic effects were found between treatments. Hence, large-effect loci indicated no trade-offs, but a shared physiology across temperatures, probably owing to the general stress response or individuals overall fitness.

evolutionary biology↗

bioRxiv2023

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird

Environmental variation can shape the gut microbiome, but majority of studies use captive-bred species, while data on large-scale variation in the gut microbiome and the associated environmental factors is lacking. Furthermore, previous studies have limited taxonomical coverage, and for example knowledge about avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species European distribution range. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall, and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.

ecology↗

bioRxiv2022

Associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings

BackgroundThe gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. ResultsGut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. ConclusionsWe found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.

ecology↗

bioRxiv2022

Variation in spontaneous mutation rate and spectrum across the genome of Neurospora crassa

While mutation rates have been extensively studied, variation in mutation rates throughout the genome is poorly understood. To understand patterns of genetic variation, it is important to understand how mutation rates vary. Chromatin modifications may be an important factor in determining variation in mutation rates in eukaryotic genomes. To study variation in mutation rates, we performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa, and sequenced the genomes of the 40 MA lines that had been propagated asexually for approximately 1015 [1003, 1026] mitoses. We detected 1322 mutations in total, and observed that the mutation rate was higher in regions of low GC, in domains of H3K9 trimethylation, in centromeric regions, and in domains of H3K27 trimethylation. The rate of single nucleotide mutations in euchromatin was 2.46 [2.19, 2.77] x 10-10. In contrast, the mutation rate in H3K9me3 domains was tenfold higher: 2.43 [2.25, 2.62] x 10-9. We also observed that the spectrum of single nucleotide mutations was different between H3K9me3 and euchromatic domains. Our statistical model of mutation rate variation predicted a moderate amount of extant genetic variation, suggesting that the mutation rate is an important factor in determining levels of natural genetic variation. Furthermore, we characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across the genome into account.

genetics↗