| 1. |
- Björklund, Mats, et al.
(författare)
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Rapid and unpredictable changes of the G-matrix in a natural bird population over 25 years
- 2013
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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 26:1, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of the genetic variances and covariances of traits (the G-matrix) is fundamental for the understanding of evolutionary dynamics of populations. Despite its essential importance in evolutionary studies, empirical tests of the temporal stability of the G-matrix in natural populations are few. We used a 25-year-long individual-based field study on almost 7000 breeding attempts of the collared flycatcher (Ficedula albicollis) to estimate the stability of the G-matrix over time. Using animal models to estimate G for several time periods, we show that the structure of the time-specific G-matrices changed significantly over time. The temporal changes in the G-matrix were unpredictable, and the structure at one time period was not indicative of the structure at the next time period. Moreover, we show that the changes in the time-specific G-matrices were not related to changes in mean trait values or due to genetic drift. Selection, differences in acquisition/allocation patterns or environment-dependent allelic effects are therefore likely explanations for the patterns observed, probably in combination. Our result cautions against assuming constancy of the G-matrix and indicates that even short-term evolutionary predictions in natural populations can be very challenging.
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| 2. |
- Bushuev, A. V., et al.
(författare)
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Quantitative genetics of basal metabolic rate and body mass in free-living pied flycatchers
- 2012
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Ingår i: Journal of Zoology. - : Wiley. - 0952-8369 .- 1469-7998. ; 288:4, s. 245-251
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Tidskriftsartikel (refereegranskat)abstract
- Despite basal metabolic rate (BMR) being one of the most commonly measured physiological traits and an important indicator of competitive ability, very little is known about its genetic basis and relation to other physiological traits. Here, we present the first attempt to estimate the multivariate basis of BMR using a natural population of pied flycatcher Ficedula hypoleuca breeding in the Tomsk Region, Western Siberia. We show relatively high and significant heritability of whole-organism BMR, mass-specific BMR and mass-independent BMR (h 2 = 0.43, 0.55 and 0.52, respectively), which indicates the potential of these energetic traits to respond to direct selection. In contrast to some previous reports, we found that the genetic correlations between body mass and all three measures of BMR were not significantly different from zero. Independent evolution of body mass and BMR in this species should therefore be possible. Following a previous report, we also estimated the genetic correlations between the different BMR measures and show they are all close to unity, suggesting that they are, from a genetic point of view, a similar trait. Our results are in contrast with previous studies measuring the genetic basis of metabolic rates using aviary-bred birds and highlight the importance of considering BMR in a natural setting.
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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- Evans, Simon R., et al.
(författare)
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Nonautosomal Genetic Variation in Carotenoid Coloration
- 2014
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Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 184:3, s. 374-383
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Tidskriftsartikel (refereegranskat)abstract
- Carotenoid-based coloration plays an important role in signaling, is often sexually dimorphic, and is potentially subject to directional and/or sex-specific selection. To understand the evolutionary dynamics of such color traits, it is essential to quantify patterns of inheritance, yet nonautosomal sources of genetic variation are easily overlooked by classical heritability analyses. Carotenoid metabolism has recently been linked to mitochondria, highlighting the potential for color variation to be explained by cytoplasmically inherited factors. In this study, we used quantitative genetic animal models to estimate the importance of mitochondrial and sex chromosome-linked sources of genetic variation in coloration in two songbird populations in which dietary carotenoids are either unmodified (great tit plumage) or metabolized into alternative color forms (zebra finch beak). We found no significant Z-linked genetic variance in great tit plumage coloration, while zebra finch beak coloration exhibited significant W linkage and cytoplasmic inheritance. Our results support cytoplasmic inheritance of color in the zebra finch, a trait based on endogenously metabolized carotenoids, and demonstrate the potential for nonautosomal sources to account for a considerable share of genetic variation in coloration. Although often overlooked, such nonautosomal genetic variation exhibits sex-dependent patterns of inheritance and potentially influences the evolution of sexual dichromatism.
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| 7. |
- Fountain, Toby, et al.
(författare)
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Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly
- 2018
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Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 11:3, s. 287-297
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Tidskriftsartikel (refereegranskat)abstract
- Dispersal is important for determining both species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville fritillary butterfly (Melitaea cinxia L.), in the Åland Islands in SW Finland. This is an ideal system to test the effectiveness of this approach due to the wealth of information already available covering dispersal across small spatial and temporal scales, but lack of information at larger spatial and temporal scales. We sampled three larvae per larval family group from 3732 groups over a six-year period and genotyped for 272 SNPs across the genome. We used this empirical data set to reconstruct cases where full-sibs were detected in different local populations to infer female effective dispersal distance, that is, dispersal events directly contributing to gene flow. On average this was one kilometre, closely matching previous dispersal estimates made using direct observation. To evaluate our power to detect full-sib families, we performed forward simulations using an individual-based model constructed and parameterized for the Glanville fritillary metapopulation. Using these simulations, 100% of predicted full-sibs were correct and over 98% of all true full-sib pairs were detected. We therefore demonstrate that even in a highly dynamic system with a relatively small number of markers, we can accurately reconstruct full-sib families and for the first time make inferences on female effective dispersal. This highlights the utility of this approach in systems where it has previously been impossible to obtain accurate estimates of dispersal over both ecological and evolutionary scales.
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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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