| 1. |
- David, Gabriel, et al.
(författare)
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Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.
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| 2. |
- DiLeo, Michelle F., et al.
(författare)
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Effects of environment and genotype on dispersal differ across departure, transfer and settlement in a butterfly metapopulation
- 2022
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 289:1976
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Tidskriftsartikel (refereegranskat)abstract
- Active dispersal is driven by extrinsic and intrinsic factors at the three stages of departure, transfer and settlement. Most empirical studies capture only one stage of this complex process, and knowledge of how much can be generalized from one stage to another remains unknown. Here we use genetic assignment tests to reconstruct dispersal across 5 years and 232 habitat patches of a Glanville fritillary butterfly (Melitaea cinxia) metapopulation. We link individual dispersal events to weather, landscape structure, size and quality of habitat patches, and individual genotype to identify the factors that influence the three stages of dispersal and post-settlement survival. We found that nearly all tested factors strongly affected departure probabilities, but that the same factors explained very little variation in realized dispersal distances. Surprisingly, we found no effect of dispersal distance on post-settlement survival. Rather, survival was influenced by weather conditions, quality of the natal habitat patch, and a strong interaction between genotype and occupancy status of the settled habitat patch, with more mobile genotypes having higher survival as colonists rather than as immigrants. Our work highlights the multi-causality of dispersal and that some dispersal costs can only be understood by considering extrinsic and intrinsic factors and their interaction across the entire dispersal process.
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| 3. |
- DiLeo, Michelle F., et al.
(författare)
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Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly
- 2018
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Ingår i: Evolution Letters. - : JOHN WILEY & SONS LTD. - 2056-3744. ; 2:6, s. 544-556
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Tidskriftsartikel (refereegranskat)abstract
- There is now clear evidence that species across a broad range of taxa harbor extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here, we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by F-st at putatively neutral loci. In a year when the population was recovering following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that (1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits and (2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.
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| 4. |
- Gudmunds, Erik, et al.
(författare)
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Contribution of ecdysone signaling to photoperiodic wing polyphenism in the water strider Gerris buenoi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Hormones play a decisive role in insect development and are central for regulating alternative life histories and phenotypic plasticity. A prominent form of plasticity is manifested in polyphenisms where discrete phenotypes, such as winged or wingless morphs, develop from the same genotype under different environmental cues. Here, hormones can induce the development of alternative morphs through interaction with specific environmental cues, e.g. nutrition, population density or photoperiod. 20-hydroxyecdysone (20E) and juvenile hormone (JH) are the two hormones which received most attention and have been shown to regulate numerous polyphenisms, for example seasonal morphs of butterflies or various castes in Hymenopterans. In this chapter we have investigated the possible role of these two hormones in the induction of alternative wing morphs in the water strider Gerris buenoi by combining RNAi, hormone injections or applications and RNA sequencing. RNAi targeting the ecdysone receptor (EcR), while highly lethal, had a significant effect on wing morph frequencies among the surviving individuals. Furthermore, analysis of RNAseq data of wing gene expression showed that many 20E-responsive genes were differentially regulated between long- and short-winged individuals. Taken together, the data presented here highlight 20E as a candidate hormone to modulate wing morph determination in G. buenoi.
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| 5. |
- Gudmunds, Erik, 1992-
(författare)
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From environmental cue to phenotypic variation – a functional investigation of wing polyphenism in an emerging model species
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phenotypic plasticity is a ubiquitous feature of living organisms and enable individuals to adapt to changing environments. A particularly prominent example of plasticity is found in polyphenisms, where environmental cues received during development leads to the generation of discrete variation in populations. In this thesis, I have studied the mechanisms underlying wing polyphenism in the water strider Gerris buenoi in order to contribute to the understanding how environmental factors can act through growth regulatory systems to induce adaptive variation. Specifically, in Paper I, I investigated which environmental factors control wing morph determination in G. buenoi and found that this species most strongly responds to variation in photoperiod conditions, but also to crowding during the juvenile stages. Exposure to challenging nutritional conditions had no effect on wing morph frequencies. Further, I found that the nutrient sensitive insulin/insulin-like growth factor signaling pathway, which have been found to regulate wing polyphenism in species where nutrition is a determinant cue for wing morph induction, has no role in regulating G. buenoi wing polyphenism, an observation in line with data showing that wing morph determination is robust to variation in nutrient conditions. In Paper II, I explored a role for the developmentally important hormones ecdysone and juvenile hormone in G. buenoi wing polyphenism. Here, I used microinjections of 20-hydroxyecdysone and topical application of methoprene, as well as RNAi against hormone receptors for ecdysone and juvenile hormone. In these experiments, I found a small but significant effect of RNAi against the ecdysone receptor, indicating that ecdysone may play a role in wing morph induction. In Paper III, I used RNA sequencing to identify candidate growth regulatory pathways for wing morph induction by photoperiod and found a significant role for the conserved Fat/Hippo pathway in G. buenoi wing morph determination. Taken together, the results presented in this thesis suggest that evolution of genetic mechanisms underlying wing polyphenism may be constrained with regard to the particular environmental cue that is used to predict the future adaptive landscape. Further, the work presented in this thesis demonstrates the power in combining sequencing methods with functional genetic tools in order to more deeply characterize the causal basis to adaptive variation, an approach to ecological and evolutionary studies which I reviewed in Paper IV.
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| 6. |
- Gudmunds, Erik, et al.
(författare)
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Functional genomic tools for emerging model species
- 2022
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Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 37:12, s. 1104-1115
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Tidskriftsartikel (refereegranskat)abstract
- Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution.
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| 7. |
- Gudmunds, Erik, et al.
(författare)
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Photoperiod controls wing polyphenism in a water strider independently of insulin receptor signalling
- 2022
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 289:1973
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Tidskriftsartikel (refereegranskat)abstract
- Insect wing polyphenism has evolved as an adaptation to changing environments and a growing body of research suggests that the nutrient-sensing insulin receptor signalling pathway is a hot spot for the evolution of polyphenisms, as it provides a direct link between growth and available nutrients in the environment. However, little is known about the potential role of insulin receptor signalling in polyphenisms which are controlled by seasonal variation in photoperiod. Here, we demonstrate that wing length polyphenism in the water strider Gerris buenoi is determined by photoperiod and nymphal density, but is not directly affected by nutrient availability. Exposure to a long-day photoperiod is highly inducive of the short-winged morph whereas high nymphal densities moderately promote the development of long wings. Using RNA interference we demonstrate that, unlike in several other species where wing polyphenism is controlled by nutrition, there is no detectable role of insulin receptor signalling in wing morph induction. Our results indicate that the multitude of possible cues that trigger wing polyphenism can be mediated through different genetic pathways and that there are multiple genetic origins to wing polyphenism in insects.
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| 8. |
- Gudmunds, Erik, et al.
(författare)
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Wing polyphenism in a water strider is caused by photoperiod-induced expression of the Fat/Hippo pathway
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The genetic mechanisms that allow organisms to incorporate information from the environment into developmental programs that control size, shape and color are important to identify in order to more fully understand developmental plasticity and adaptation to changing environments. Insect polyphenisms provide good models to study such mechanisms because environmental factors are the main source of variation in the trait of study. Here we studied the regulatory mechanism that controls wing length polyphenism in the water strider Gerris buenoi, which is primarily controlled by variation in photoperiod. By sequencing RNA sampled from wing buds across development in different photoperiodic conditions (and therefore alternative wing developmental trajectories) we found that differences in transcriptional activity arose primarily in the late 5th instar stage. Among the differentially expressed genes, the Fat/Hippo and ecdysone signaling pathways, both putative growth regulatory mechanisms that could underlie wing morph determination, were among those that showed significant enrichment. We therefore used RNA interference against the differentially expressed genes Fat, Dachsous and Yorkie to assess whether they play a causative role in photoperiod induced wing length variation in Gerris buenoi. Our results suggest that the conserved Fat/Hippo pathway is a key regulatory network involved in the control of wing polyphenism in this species. Therefore, photoperiod induces wing polyphenism in Gerris buenoi through its regulation of the Fat/Hippo pathway. This study provides an important basis for future comparative studies on the evolution of wing polyphenism and furthers our understanding of the genetic regulation of this process in insects.
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| 9. |
- Husby, Arild, Associate Senior Lecturer
(författare)
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On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies
- 2020
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Ingår i: Integrative and Comparative Biology. - : OXFORD UNIV PRESS INC. - 1540-7063 .- 1557-7023. ; 60:6, s. 1558-1566
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Tidskriftsartikel (refereegranskat)abstract
- There is increasing interest in understanding the potential for epigenetic factors to contribute to phenotypic diversity in evolutionary biology. One well studied epigenetic mechanism is DNA methylation, the addition of a methyl group to cytosines, which have the potential to alter gene expression depending on the genomic region in which it takes place. Obtaining information about DNA methylation at genome-wide scale has become straightforward with the use of bisulfite treatment in combination with reduced representation or whole-genome sequencing. While it is well recognized that methylation is tissue specific, a frequent limitation for many studies is that sampling-specific tissues may require sacrificing individuals, something which is generally undesirable and sometimes impossible. Instead, information about DNA methylation patterns in the blood is frequently used as a proxy tissue. This can obviously be problematic if methylation patterns in the blood do not reflect that in the relevant tissue. Understanding how, or if, DNA methylation in blood reflect DNA methylation patterns in other tissues is therefore of utmost importance if we are to make inferences about how observed differences in methylation or temporal changes in methylation can contribute to phenotypic variation. The aim of this review is to examine what we know about the potential for using blood samples in ecological epigenetic studies. I briefly outline some methods by which we can measure DNA methylation before I examine studies that have compared DNA methylation patterns across different tissues and, finally, examine how useful blood samples may be for ecological studies of DNA methylation. Ecological epigenetic studies are in their infancy, but it is paramount for the field to move forward to have detailed information about tissue and time dependence relationships in methylation to gain insights into if blood DNA methylation patterns can be a reliable bioindicator for changes in methylation that generate phenotypic variation in ecologically important traits.
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| 10. |
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| 11. |
- Husby, Arild, Associate Senior Lecturer
(författare)
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Wild epigenetics : insights from epigenetic studies on natural populations
- 2022
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8452 .- 1471-2954. ; 289:1968
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Forskningsöversikt (refereegranskat)abstract
- Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are increasingly targeted in studies of natural populations. Here, I review some of the insights gained from this research, examine some of the methods currently in use and discuss some of the challenges that researchers working on natural populations are likely to face when probing epigenetic mechanisms. While studies supporting the involvement of epigenetic mechanisms in generating phenotypic variation in natural populations are amassing, many of these studies are currently correlative in nature. Thus, while empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation. Disentangling these two sources of variation will be a key to resolving the debate about the importance of epigenetic mechanisms, and studies on natural populations that partition the relative contribution of genetic and epigenetic factors to phenotypic variation can play an important role in this debate.
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| 12. |
- Kaufmann, Philipp, et al.
(författare)
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Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance
- 2021
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Ingår i: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X. ; 5:10, s. 1394-1402
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Tidskriftsartikel (refereegranskat)abstract
- Sexual dimorphism is ubiquitous in nature but its evolution is puzzling given that the mostly shared genome constrains independent evolution in the sexes. Sex differences should result from asymmetries between the sexes in selection or genetic variation but studies investigating both simultaneously are lacking. Here, we combine a quantitative genetic analysis of body size variation, partitioned into autosomal and sex chromosome contributions and ten generations of experimental evolution to dissect the evolution of sexual body size dimorphism in seed beetles (Callosobruchus maculatus) subjected to sexually antagonistic or sex-limited selection. Female additive genetic variance (VA) was primarily linked to autosomes, exhibiting a strong intersexual genetic correlation with males (?am,f = 0.926), while X- and Y-linked genes further contributed to the male VA and X-linked genes contributed to female dominance variance. Consistent with these estimates, sexual body size dimorphism did not evolve in response to female-limited selection but evolved by 30–50% under male-limited and sexually antagonistic selection. Remarkably, Y-linked variance alone could change dimorphism by 30%, despite the C. maculatus Y chromosome being small and heterochromatic. Our results demonstrate how the potential for sexual dimorphism to evolve depends on both its underlying genetic basis and the nature of sex-specific selection.
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| 13. |
- Kemppainen, Petri, et al.
(författare)
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Accounting for heteroscedasticity and censoring in chromosome partitioning analyses
- 2018
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Ingår i: Evolution Letters. - : JOHN WILEY & SONS LTD. - 2056-3744. ; 2:6, s. 599-609
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Tidskriftsartikel (refereegranskat)abstract
- A fundamental assumption in quantitative genetics is that traits are controlled by many loci of small effect. Using genomic data, this assumption can be tested using chromosome partitioning analyses, where the proportion of genetic variance for a trait explained by each chromosome (h(c)(2)), is regressed on its size. However, as h(c)(2)-estimates are necessarily positive (censoring) and the variance increases with chromosome size (heteroscedasticity), two fundamental assumptions of ordinary least squares (OLS) regression are violated. Using simulated and empirical data we demonstrate that these violations lead to incorrect inference of genetic architecture. The degree of bias depends mainly on the number of chromosomes and their size distribution and is therefore specific to the species; using published data across many different species we estimate that not accounting for this effect overall resulted in 28% false positives. We introduce a new and computationally efficient resampling method that corrects for inflation caused by heteroscedasticity and censoring and that works under a large range of dataset sizes and genetic architectures in empirical datasets. Our new method substantially improves the robustness of inferences from chromosome partitioning analyses.
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| 14. |
- Kemppainen, Petri, et al.
(författare)
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Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution
- 2018
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Ingår i: Molecular Ecology Resources. - : WILEY. - 1755-098X .- 1755-0998. ; 18:4, s. 767-777
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Tidskriftsartikel (refereegranskat)abstract
- Genomewide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so-called "chromosome partitioning" where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes. Nor has the influence of sample size, heritability of the trait, effect size distribution of loci controlling the trait or the physical distribution of the causal loci in the genome been examined. Using simulated data, we show that these characteristics have major influence on the inferences of the genetic architecture of traits we can infer using chromosome partitioning analyses. In particular, small variation in chromosome size, small sample size, low heritability, a skewed effect size distribution and clustering of loci can lead to a loss of power and consequently altered inference from chromosome partitioning analyses. Future studies employing this approach need to consider and derive an appropriate null model for their study system, taking these parameters into consideration. Our simulation results can provide some guidelines on these matters, but further studies examining a broader parameter space are needed.
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| 15. |
- Kochanova, Elena, et al.
(författare)
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Patterns of Cryptic Diversity and Phylogeography in Four Freshwater Copepod Crustaceans in European Lakes
- 2021
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Ingår i: Diversity. - : MDPI. - 1424-2818. ; 13:9
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Tidskriftsartikel (refereegranskat)abstract
- Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversity within widespread species and understanding how historical and biogeographical factors shape the modern patterns of their distribution. Most comparative phylogeographic studies so far focus on terrestrial and vertebrate taxa, while aquatic invertebrates (and especially freshwater invertebrates) remain unstudied. In this article, we explore and compare the patterns of molecular diversity and phylogeographic structure of four widespread freshwater copepod crustaceans in European water bodies: the harpacticoids Attheyella crassa, Canthocamptus staphylinus and Nitokra hibernica, and the cyclopoid Eucyclops serrulatus, using sequence data from mtDNA COI and nuclear ITS/18S rRNA genes. The three taxa A. crassa, C. staphylinus and E. serrulatus each consist of deeply diverged clusters and are deemed to represent complexes of species with largely (but not completely) non-overlapping distributions, while in N. hibernica only little differentiation was found, which may however reflect the geographically more restricted sampling. However, the geographical patterns of subdivision differ. The divisions in A. crassa and E. serrulatus follow an east-west pattern in Northern Europe whereas that in C. staphylinus has more of a north-south pattern, with a distinct Fennoscandian clade. The deep mitochondrial splits among populations of A. crassa, C. staphylinus and E. serrulatus (model-corrected distances 26-36%) suggest that divergence of the lineages predate the Pleistocene glaciations. This study provides an insight into cryptic diversity and biogeographic distribution of freshwater copepods.
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| 16. |
- Lindner, Melanie, et al.
(författare)
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Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:15, s. 3645-3659
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Tidskriftsartikel (refereegranskat)abstract
- Species with a circannual life cycle need to match the timing of their life history events to the environment to maximize fitness. However, our understanding of how circannual traits such as timing of reproduction are regulated on a molecular level remains limited. Recent studies have implicated that epigenetic mechanisms can be an important part in the processes that regulate circannual traits. Here, we explore the role of DNA methylation in mediating reproductive timing in a seasonally breeding bird species, the great tit (Parus major), using genome-wide DNA methylation data from individual females that were blood sampled repeatedly throughout the breeding season. We demonstrate rapid and directional changes in DNA methylation within the promoter region of several genes, including a key transcription factor (NR5A1) known from earlier studies to be involved in the initiation of timing of reproduction. Interestingly, the observed changes in DNA methylation at NR5A1 identified here are in line with earlier gene expression studies of reproduction in chicken, indicating that the observed shifts in DNA methylation at this gene can have a regulatory role. Our findings provide an important step towards elucidating the genomic mechanism that mediates seasonal timing of a key life history traits and provide support for the idea that epigenetic mechanisms may play an important role in circannual traits.
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| 17. |
- Lindner, Melanie, et al.
(författare)
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Temporal changes in DNA methylation and RNA expression in a small song bird : within- and between-tissue comparisons
- 2021
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n=6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.Results: We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10kb up- and downstream regions adjacent to the gene body.Conclusion: Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.
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| 18. |
- Lundregan, Sarah L., et al.
(författare)
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Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow
- 2022
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Ingår i: Ecology and Evolution. - : Wiley-Blackwell. - 2045-7758. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- Parasites can exert strong selective pressures on their hosts and influence the evolution of host immunity. While several studies have examined the genetic basis for parasite resistance, the role of epigenetics in the immune response to parasites is less understood. Yet, epigenetic modifications, such as changes in DNA methylation, may allow species to respond rapidly to parasite prevalence or virulence. To test the role of DNA methylation in relation to parasite infection, we examined genome-wide DNA methylation before and during infection by a parasitic nematode, Syngamus trachea, in a natural population of house sparrows (Passer domesticus) using reduced representation bisulfite sequencing (RRBS). We found that DNA methylation levels were slightly lower in infected house sparrows, and we identified candidate genes relating to the initial immune response, activation of innate and adaptive immunity, and mucus membrane functional integrity that were differentially methylated between infected and control birds. Subsequently, we used methylation-sensitive high-resolution melting (MS-HRM) analyses to verify the relationship between methylation proportion and S. trachea infection status at two candidate genes in a larger sample dataset. We found that methylation level at NR1D1, but not CLDN22, remained related to infection status and that juvenile recruitment probability was positively related to methylation level at NR1D1. This underscores the importance of performing follow-up studies on candidate genes. Our findings demonstrate that plasticity in the immune response to parasites can be epigenetically mediated and highlight the potential for epigenetic studies in natural populations to provide further mechanistic insight into host-parasite interactions.
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| 19. |
- Lundregan, Sarah L., et al.
(författare)
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Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis
- 2018
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 27:17, s. 3498-3514
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the genetic architecture of quantitative traits can provide insights into the mechanisms driving phenotypic evolution. Bill morphology is an ecologically important and phenotypically variable trait, which is highly heritable and closely linked to individual fitness. Thus, bill morphology traits are suitable candidates for gene mapping analyses. Previous studies have revealed several genes that may influence bill morphology, but the similarity of gene and allele effects between species and populations is unknown. Here, we develop a custom 200K SNP array and use it to examine the genetic basis of bill morphology in 1857 house sparrow individuals from a large-scale, island metapopulation off the coast of Northern Norway. We found high genomic heritabilities for bill depth and length, which were comparable with previous pedigree estimates. Candidate gene and genomewide association analyses yielded six significant loci, four of which have previously been associated with craniofacial development. Three of these loci are involved in bone morphogenic protein (BMP) signalling, suggesting a role for BMP genes in regulating bill morphology. However, these loci individually explain a small amount of variance. In combination with results from genome partitioning analyses, this indicates that bill morphology is a polygenic trait. Any studies of eco-evolutionary processes in bill morphology are therefore dependent on methods that can accommodate polygenic inheritance of the phenotype and molecular-scale evolution of genetic architecture.
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| 20. |
- Lundregan, Sarah L., et al.
(författare)
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Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge
- 2020
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29:20, s. 3812-3829
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Tidskriftsartikel (refereegranskat)abstract
- Host-parasite relationships are likely to change over the coming decades in response to climate change and increased anthropogenic stressors. Understanding the genetic architecture of parasite resistance will aid prediction of species' responses to intensified parasite challenge. The gapeworm "Syngamus trachea" is prevalent in natural bird populations and causes symptomatic infections ranging from mild to severe. The parasite may affect ecological processes by curtailing bird populations and is important due to its propensity to spread to commercially farmed birds. Our large-scale data set on an insular house sparrow metapopulation in northern Norway includes information on gapeworm prevalence and infection intensity, allowing assessment of the genetics of parasite resistance in a natural system. To determine whether parasite resistance has a heritable genetic component, we performed variance component analyses using animal models. Resistance to gapeworm had substantial additive genetic and dominance variance, and genome-wide association studies to identify single nucleotide polymorphisms associated with gapeworm resistance yielded multiple loci linked to immune function. Together with genome partitioning results, this indicates that resistance to gapeworm is under polygenic control in the house sparrow, and probably in other bird species. Hence, our results provide the foundation needed to study any eco-evolutionary processes related to gapeworm infection, and show that it is necessary to use methods suitable for polygenic and nonadditive genetic effects on the phenotype.
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| 21. |
- Mäkinen, Hannu, et al.
(författare)
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Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing
- 2019
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Ingår i: Scientific Data. - : NATURE PUBLISHING GROUP. - 2052-4463. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Seasonal timing of reproduction is an important fitness trait in many plants and animals but the underlying molecular mechanism for this trait is poorly known. DNA methylation is known to affect timing of reproduction in various organisms and is therefore a potential mechanism also in birds. Here we describe genome wide data aiming to detect temporal changes in methylation in relation to timing of breeding using artificial selection lines of great tits (Parus major) exposed to contrasting temperature treatments. Methylation levels of DNA extracted from erythrocytes were examined using reduced representation bisulfite sequencing (RRBS). In total, we obtained sequencing data from 63 libraries over four different time points from 16 birds with on average 20 million quality filtered reads per library. These data describe individual level temporal variation in DNA methylation throughout the breeding season under experimental temperature regimes and provides a resource for future studies investigating the role of temporal changes in DNA methylation in timing of reproduction.
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| 22. |
- Niskanen, Alina K., et al.
(författare)
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Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:25, s. 14584-14592
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Tidskriftsartikel (refereegranskat)abstract
- Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
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| 23. |
- Qvarnström, Anna, et al.
(författare)
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Assortative Mating in an Ecological Context : Effects of Mate Choice Errors and Relative Species Abundance on the Frequency and Asymmetry of Hybridization
- 2023
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 201:1, s. 125-137
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Tidskriftsartikel (refereegranskat)abstract
- The frequency and asymmetry of mixed-species mating set the initial stage for the ecological and evolutionary implications of hybridization. How such patterns of mixed-species mating, in turn, are influenced by the combination of mate choice errors and relative species abundance remains largely unknown. We develop a mathematical model that generates predictions for how relative species abundances and mate choice errors affect hybridization patterns. When mate choice errors are small (<5%), the highest frequency of hybridization occurs when one of the hybridizing species is at low abundance, but when mate choice errors are high (>5%), the highest hybridization frequency occurs when species occur in equal proportions. Furthermore, females of the less abundant species are overrepresented in mixed-species matings. We compare our theoretical predictions with empirical data on naturally hybridizing Ficedula flycatchers and find that hybridization is highest when the two species occur in equal abundance, implying rather high mate choice errors. We discuss ecological and evolutionary implications of our findings and encourage future work on hybrid zone dynamics that take demographic aspects, such as relative species abundance, into account.
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| 24. |
- Raulo, Aura, et al.
(författare)
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Social networks strongly predict the gut microbiota of wild mice
- 2021
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Ingår i: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 15:9, s. 2601-2613
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Tidskriftsartikel (refereegranskat)abstract
- The mammalian gut teems with microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains underexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.
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| 25. |
- Rogell, Björn, et al.
(författare)
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Controlling for body size leads to inferential biases in the biological sciences
- 2020
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Ingår i: Evolution Letters. - : Oxford University Press (OUP). - 2056-3744. ; 4:1, s. 73-82
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Tidskriftsartikel (refereegranskat)abstract
- Many traits correlate with body size. Studies that seek to uncover the ecological factors that drive evolutionary responses in traits typically examine these responses relative to associated changes in body size using multiple regression analysis. However, it is not well appreciated that in the presence of strongly correlated variables, the partial (i.e., relative) regression coefficients often change sign compared to the original coefficients. Such sign reversals are difficult to interpret in a biologically meaningful way, and could lead to erroneous evolutionary inferences if the true mechanism underlying the sign reversal differed from the proposed mechanism. Here, we use simulations to demonstrate that sign reversal occurs over a wide range of parameter values common in the biological sciences. Further, as a case-in-point, we review the literature on brain size evolution; a field that explores how ecological traits relate to the evolution of relative brain size (brain size relative to body size). We find that most studies show sign reversals and thus that the inferences of many studies in this field may be inconclusive. Finally, we propose some approaches to mitigating this issue.
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