1
|
David G, Bertolotti A, Layer R, Scofield D, Hayward A, Baril T, Burnett HA, Gudmunds E, Jensen H, Husby A. Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations. Genome Biol Evol 2024; 16:evae049. [PMID: 38489588 PMCID: PMC11018544 DOI: 10.1093/gbe/evae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
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.
Collapse
Affiliation(s)
- Gabriel David
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Ryan Layer
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Douglas Scofield
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Hamish A Burnett
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Erik Gudmunds
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| |
Collapse
|
2
|
Saatoglu D, Lundregan SL, Fetterplace E, Goedert D, Husby A, Niskanen AK, Muff S, Jensen H. The genetic basis of dispersal in a vertebrate metapopulation. Mol Ecol 2024; 33:e17295. [PMID: 38396362 DOI: 10.1111/mec.17295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbour adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single-nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), and found a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythm, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA 2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA 2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA 2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal and demonstrate that adaptive potential may be environment dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.
Collapse
Affiliation(s)
- Dilan Saatoglu
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sarah L Lundregan
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Evelyn Fetterplace
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Debora Goedert
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Alina K Niskanen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Stefanie Muff
- Department of Mathematical Sciences, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
3
|
Wanelik KM, Raulo A, Troitsky T, Husby A, Knowles SCL. Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice. Anim Microbiome 2023; 5:29. [PMID: 37259168 DOI: 10.1186/s42523-023-00247-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND The mammalian gut microbiota influences a wide array of phenotypes which are relevant to fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life. RESULTS We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we identify a candidate maternally-transmitted bacterial family in wood mice, the Muribaculaceae. CONCLUSION Overall, our findings point to an ontogenetically shifting transmission landscape in wild mice, with a mother's influence on microbiota composition waning as offspring age, while the relative impact of social contacts grows.
Collapse
Affiliation(s)
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK
- Department of Computing, University of Turku, Turku, Finland
| | | | - Arild Husby
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | |
Collapse
|
4
|
Qvarnström A, Veen T, Husby A, Ålund M, Weissing FJ. Assortative Mating in an Ecological Context: Effects of Mate Choice Errors and Relative Species Abundance on the Frequency and Asymmetry of Hybridization. Am Nat 2023; 201:125-137. [PMID: 36524936 DOI: 10.1086/722156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe 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.
Collapse
|
5
|
Lundregan SL, Mäkinen H, Buer A, Holand H, Jensen H, Husby A. Infection by a helminth parasite is associated with changes in
DNA
methylation in the house sparrow. Ecol Evol 2022; 12:e9539. [PMCID: PMC9702581 DOI: 10.1002/ece3.9539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sarah L. Lundregan
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Hannu Mäkinen
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Evolutionary Biology, Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Amberly Buer
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Håkon Holand
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Arild Husby
- Department of Biology, Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Evolutionary Biology, Department of Ecology and Genetics Uppsala University Uppsala Sweden
| |
Collapse
|
6
|
DiLeo MF, Nonaka E, Husby A, Saastamoinen M. Effects of environment and genotype on dispersal differ across departure, transfer and settlement in a butterfly metapopulation. Proc Biol Sci 2022; 289:20220322. [PMID: 35673865 PMCID: PMC9174707 DOI: 10.1098/rspb.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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.
Collapse
Affiliation(s)
- Michelle F. DiLeo
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland,Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Peterborough, ON, Canada
| | - Etsuko Nonaka
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Marjo Saastamoinen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| |
Collapse
|
7
|
Gudmunds E, Narayanan S, Lachivier E, Duchemin M, Khila A, Husby A. Photoperiod controls wing polyphenism in a water strider independently of insulin receptor signalling. Proc Biol Sci 2022; 289:20212764. [PMID: 35473377 PMCID: PMC9043737 DOI: 10.1098/rspb.2021.2764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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.
Collapse
Affiliation(s)
- Erik Gudmunds
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Shrinath Narayanan
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Elise Lachivier
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Marion Duchemin
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Abderrahman Khila
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden.,Centre for Biodiversity Dynamics, Norwegian University for Science and Technology, Trondheim, Norway
| |
Collapse
|
9
|
Kaufmann P, Wolak ME, Husby A, Immonen E. Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance. Nat Ecol Evol 2021; 5:1394-1402. [PMID: 34413504 DOI: 10.1038/s41559-021-01530-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023]
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 ([Formula: see text] = 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.
Collapse
Affiliation(s)
- Philipp Kaufmann
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - Matthew E Wolak
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Elina Immonen
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
10
|
Saatoglu D, Niskanen AK, Kuismin M, Ranke PS, Hagen IJ, Araya-Ajoy YG, Kvalnes T, Pärn H, Rønning B, Ringsby TH, Saether BE, Husby A, Sillanpää MJ, Jensen H. Dispersal in a house sparrow metapopulation: An integrative case study of genetic assignment calibrated with ecological data and pedigree information. Mol Ecol 2021; 30:4740-4756. [PMID: 34270821 DOI: 10.1111/mec.16083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 01/12/2023]
Abstract
Dispersal has a crucial role determining ecoevolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (Passer domesticus) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of interpopulation genetic differentiation, intrapopulation genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.
Collapse
Affiliation(s)
- Dilan Saatoglu
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alina K Niskanen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Markku Kuismin
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Finland
| | - Peter S Ranke
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingerid J Hagen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Norwegian Institute for Nature Research, Trondheim, Norway
| | - Yimen G Araya-Ajoy
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Henrik Pärn
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bernt Rønning
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thor Harald Ringsby
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bernt-Erik Saether
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Mikko J Sillanpää
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Finland.,Infotech Oulu, University of Oulu, Oulu, Finland
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
11
|
Raulo A, Allen BE, Troitsky T, Husby A, Firth JA, Coulson T, Knowles SCL. Social networks strongly predict the gut microbiota of wild mice. ISME J 2021; 15:2601-2613. [PMID: 33731838 PMCID: PMC8397773 DOI: 10.1038/s41396-021-00949-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
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.
Collapse
Affiliation(s)
- Aura Raulo
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Bryony E Allen
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Tanya Troitsky
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Arild Husby
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Josh A Firth
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
| | | |
Collapse
|
12
|
Lindner M, Laine VN, Verhagen I, Viitaniemi HM, Visser ME, van Oers K, Husby A. Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird. Mol Ecol 2021; 30:3645-3659. [PMID: 33453134 PMCID: PMC8359384 DOI: 10.1111/mec.15803] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/06/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022]
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. see also the Perspective by Melanie J. Heckwolf and Britta S. Meyer
Collapse
Affiliation(s)
- Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Heidi M Viitaniemi
- Organismal and Evolutionary Biology Research Programme (OEB), University of Helsinki, Helsinki, Finland
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme (OEB), University of Helsinki, Helsinki, Finland.,Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway.,Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
13
|
Lindner M, Verhagen I, Viitaniemi HM, Laine VN, Visser ME, Husby A, van Oers K. Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons. BMC Genomics 2021; 22:36. [PMID: 33413102 PMCID: PMC7792223 DOI: 10.1186/s12864-020-07329-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022] Open
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 10 kb 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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07329-9.
Collapse
Affiliation(s)
- Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700, AB, The Netherlands. .,Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700, AB, The Netherlands.,Wageningen University & Research, Wageningen, The Netherlands
| | - Heidi M Viitaniemi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Vertebrate Biology, Czech Academy of Sciences, Prague, Czech Republic.,Department of Biology, University of Turku, Turku, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700, AB, The Netherlands.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700, AB, The Netherlands.,Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Department of Biology, NTNU, Centre for Biodiversity Dynamics, Trondheim, Norway
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700, AB, The Netherlands.
| |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, SE-75236 Uppsala, Sweden
| |
Collapse
|
15
|
Lundregan SL, Niskanen AK, Muff S, Holand H, Kvalnes T, Ringsby T, Husby A, Jensen H. Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge. Mol Ecol 2020; 29:3812-3829. [DOI: 10.1111/mec.15491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sarah L. Lundregan
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Stefanie Muff
- Centre for Biodiversity Dynamics Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| | - Håkon Holand
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thor‐Harald Ringsby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Evolutionary Biology Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| |
Collapse
|
16
|
|
17
|
Rogell B, Dowling DK, Husby A. Controlling for body size leads to inferential biases in the biological sciences. Evol Lett 2019; 4:73-82. [PMID: 32055413 PMCID: PMC7006466 DOI: 10.1002/evl3.151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 10/14/2019] [Accepted: 10/20/2019] [Indexed: 01/15/2023] Open
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.
Collapse
Affiliation(s)
- Björn Rogell
- Department of Zoology Stockholm University Svante Arrhenius väg 18 Stockholm Sweden.,Department of Aquatic Resources, Institute of Freshwater Research Swedish University of Agricultural Sciences Drottningholm 17893 Sweden
| | - Damian K Dowling
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
| | - Arild Husby
- Centre for Biodiversity Dynamics Norwegian University of Science and Technology 7491 Trondheim Norway.,Evolutionary Biology, Department of Ecology and Genetics Uppsala University 75236 Uppsala Sweden
| |
Collapse
|
18
|
Mäkinen H, Viitaniemi HM, Visser ME, Verhagen I, van Oers K, Husby A. Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing. Sci Data 2019; 6:136. [PMID: 31341168 PMCID: PMC6656709 DOI: 10.1038/s41597-019-0136-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 06/19/2019] [Indexed: 12/28/2022] Open
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.
Collapse
Affiliation(s)
- Hannu Mäkinen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway.
| | - Heidi M Viitaniemi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway.
| |
Collapse
|
19
|
Viitaniemi HM, Verhagen I, Visser ME, Honkela A, van Oers K, Husby A. Seasonal Variation in Genome-Wide DNA Methylation Patterns and the Onset of Seasonal Timing of Reproduction in Great Tits. Genome Biol Evol 2019; 11:970-983. [PMID: 30840074 PMCID: PMC6447391 DOI: 10.1093/gbe/evz044] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
In seasonal environments, timing of reproduction is a trait with important fitness consequences, but we know little about the molecular mechanisms that underlie the variation in this trait. Recently, several studies put forward DNA methylation as a mechanism regulating seasonal timing of reproduction in both plants and animals. To understand the involvement of DNA methylation in seasonal timing of reproduction, it is necessary to examine within-individual temporal changes in DNA methylation, but such studies are very rare. Here, we use a temporal sampling approach to examine changes in DNA methylation throughout the breeding season in female great tits (Parus major) that were artificially selected for early timing of breeding. These females were housed in climate-controlled aviaries and subjected to two contrasting temperature treatments. Reduced representation bisulfite sequencing on red blood cell derived DNA showed genome-wide temporal changes in more than 40,000 out of the 522,643 CpG sites examined. Although most of these changes were relatively small (mean within-individual change of 6%), the sites that showed a temporal and treatment-specific response in DNA methylation are candidate sites of interest for future studies trying to understand the link between DNA methylation patterns and timing of reproduction.
Collapse
Affiliation(s)
- Heidi M Viitaniemi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Finland
- Department of Public Health, University of Helsinki, Finland
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Department of Ecology and Genetics, EBC, Uppsala University, Sweden
- Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
| |
Collapse
|
20
|
DiLeo MF, Husby A, Saastamoinen M. Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly. Evol Lett 2018; 2:544-556. [PMID: 30564438 PMCID: PMC6292703 DOI: 10.1002/evl3.90] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
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 Fst 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.
Collapse
Affiliation(s)
- Michelle F. DiLeo
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
| | - Arild Husby
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
- Department of Evolutionary Biology, EBCUppsala UniversityNorbyvägen 18D75236UppsalaSweden
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
| |
Collapse
|
21
|
Kemppainen P, Husby A. Accounting for heteroscedasticity and censoring in chromosome partitioning analyses. Evol Lett 2018; 2:599-609. [PMID: 30564443 PMCID: PMC6292708 DOI: 10.1002/evl3.88] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 01/02/2023] Open
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 (h2c), is regressed on its size. However, as h2c‐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.
Collapse
Affiliation(s)
- Petri Kemppainen
- Organismal and Evolutionary Biology Research Programme University of Helsinki 00014 Helsinki Finland
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme University of Helsinki 00014 Helsinki Finland.,Department of Ecology and Genetics Uppsala University 75236 Uppsala Sweden
| |
Collapse
|
22
|
Lundregan SL, Hagen IJ, Gohli J, Niskanen AK, Kemppainen P, Ringsby TH, Kvalnes T, Pärn H, Rønning B, Holand H, Ranke PS, Båtnes AS, Selvik LK, Lien S, Saether BE, Husby A, Jensen H. Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis. Mol Ecol 2018; 27:3498-3514. [DOI: 10.1111/mec.14811] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sarah L. Lundregan
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Ingerid J. Hagen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Norwegian Institute for Nature Research; Trondheim Norway
| | - Jostein Gohli
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Alina K. Niskanen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Department of Ecology and Genetics; University of Oulu; Oulu Finland
| | - Petri Kemppainen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Thor Harald Ringsby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Thomas Kvalnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Henrik Pärn
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Bernt Rønning
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Håkon Holand
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Peter S. Ranke
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Anna S. Båtnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Linn-Karina Selvik
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics; Department of Animal and Aquacultural Sciences; Faculty of Life Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Bernt-Erik Saether
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Arild Husby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
- Department of Ecology and Genetics; EBC; Uppsala University; Uppsala Sweden
| | - Henrik Jensen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| |
Collapse
|
23
|
Kemppainen P, Husby A. Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution. Mol Ecol Resour 2018. [DOI: 10.1111/1755-0998.12774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Petri Kemppainen
- Metapopulation Research Centre Department of Biosciences University of Helsinki Helsinki Finland
| | - Arild Husby
- Metapopulation Research Centre Department of Biosciences University of Helsinki Helsinki Finland
- Department of Ecology and Genetics (Evolutionary Biology) EBC Uppsala University Uppsala Sweden
| |
Collapse
|
24
|
Fountain T, Husby A, Nonaka E, DiLeo MF, Korhonen JH, Rastas P, Schulz T, Saastamoinen M, Hanski I. Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly. Evol Appl 2017. [DOI: 10.1111/eva.12552] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Toby Fountain
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Arild Husby
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Etsuko Nonaka
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Biology; Lund University; Lund Sweden
| | | | - Janne H. Korhonen
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Computer Science; Aalto University; Aalto Finland
| | - Pasi Rastas
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Zoology; University of Cambridge; Cambridge UK
| | - Torsti Schulz
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | | | - Ilkka Hanski
- Department of Biosciences; University of Helsinki; Helsinki Finland
| |
Collapse
|
25
|
Saastamoinen M, Bocedi G, Cote J, Legrand D, Guillaume F, Wheat CW, Fronhofer EA, Garcia C, Henry R, Husby A, Baguette M, Bonte D, Coulon A, Kokko H, Matthysen E, Niitepõld K, Nonaka E, Stevens VM, Travis JMJ, Donohue K, Bullock JM, Del Mar Delgado M. Genetics of dispersal. Biol Rev Camb Philos Soc 2017; 93:574-599. [PMID: 28776950 PMCID: PMC5811798 DOI: 10.1111/brv.12356] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/12/2022]
Abstract
Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.
Collapse
Affiliation(s)
- Marjo Saastamoinen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | - Julien Cote
- Laboratoire Évolution & Diversité Biologique UMR5174, CNRS, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Delphine Legrand
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Christopher W Wheat
- Population Genetics, Department of Zoology, Stockholm University, S-10691 Stockholm, Sweden
| | - Emanuel A Fronhofer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland
| | - Cristina Garcia
- CIBIO-InBIO, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Roslyn Henry
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K.,School of GeoSciences, University of Edinburgh, Edinburgh EH89XP, U.K
| | - Arild Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Michel Baguette
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France.,Museum National d'Histoire Naturelle, Institut Systématique, Evolution, Biodiversité, UMR 7205, F-75005 Paris, France
| | - Dries Bonte
- Department of Biology, Ghent University, B-9000 Ghent, Belgium
| | - Aurélie Coulon
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des Vertébrés, 34293 Montpellier, France.,CESCO UMR 7204, Bases écologiques de la conservation, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Kristjan Niitepõld
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Etsuko Nonaka
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Justin M J Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | | | - James M Bullock
- NERC Centre for Ecology & Hydrology, Wallingford OX10 8BB, U.K
| | | |
Collapse
|
26
|
Schultz JK, Wallon C, Blecic L, Forsmo HM, Folkesson J, Buchwald P, Kørner H, Dahl FA, Øresland T, Yaqub S, Papp A, Ersson U, Zittel T, Fagerström N, Gustafsson D, Dafnis G, Cornelius M, Egenvall M, Nyström PO, Syk I, Vilhjalmsson D, Arbman G, Chabok A, Helgeland M, Bondi J, Husby A, Helander R, Kjos A, Gregussen H, Talabani AJ, Tranø G, Nygaard IH, Wiedswang G, Sjo OH, Desserud KF, Norderval S, Gran MV, Pettersen T, Sæther A. One-year results of the SCANDIV randomized clinical trial of laparoscopic lavage versus primary resection for acute perforated diverticulitis. Br J Surg 2017. [DOI: 10.1002/bjs.10567] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Background
Recent randomized trials demonstrated that laparoscopic lavage compared with resection for Hinchey III perforated diverticulitis was associated with similar mortality, less stoma formation but a higher rate of early reintervention. The aim of this study was to compare 1-year outcomes in patients who participated in the randomized Scandinavian Diverticulitis (SCANDIV) trial.
Methods
Between February 2010 and June 2014, patients from 21 hospitals in Norway and Sweden presenting with suspected perforated diverticulitis were enrolled in a multicentre RCT comparing laparoscopic lavage and sigmoid resection. All patients with perforated diverticulitis confirmed during surgery were included in a modified intention-to-treat analysis of 1-year results.
Results
Of 199 enrolled patients, 101 were assigned randomly to laparoscopic lavage and 98 to colonic resection. Perforated diverticulitis was confirmed at the time of surgery in 89 and 83 patients respectively. Within 1 year after surgery, neither severe complications (34 versus 27 per cent; P = 0·323) nor disease-related mortality (12 versus 11 per cent) differed significantly between the lavage and surgery groups. Among the 144 patients with purulent peritonitis, the rate of severe complications (27 per cent (20 of 74) versus 21 per cent (15 of 70) respectively; P = 0·445) and disease-related mortality (8 versus 9 per cent) were similar. Laparoscopic lavage was associated with more deep surgical-site infections (32 versus 13 per cent; P = 0·006) but fewer superficial surgical-site infections (1 versus 17 per cent; P = 0·001). More patients in the lavage group underwent unplanned reoperations (27 versus 10 per cent; P = 0·010). Including stoma reversals, a similar proportion of patients required a secondary operation (28 versus 29 per cent). The stoma rate at 1 year was lower in the lavage group (14 versus 42 per cent in the resection group; P < 0·001); however, the Cleveland Global Quality of Life score did not differ between groups.
Conclusion
The advantages of laparoscopic lavage should be weighed against the risk of secondary intervention (if sepsis is unresolved). Assessment to exclude malignancy (although uncommon) is advised. Registration number: NCT01047462 (http://www.clinicaltrials.gov).
Collapse
Affiliation(s)
| | - J K Schultz
- Department of Gastrointestinal Surgery, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - C Wallon
- Department of Surgery and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - L Blecic
- Department of Gastrointestinal Surgery, Østfold Hospital Kalnes, Fredrikstad, Norway
| | - H M Forsmo
- Department of Gastrointestinal and Emergency Surgery, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - J Folkesson
- Colorectal Surgery Unit, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - P Buchwald
- Colorectal Unit, Department of Surgery, Skåne University Hospital Malmö, Malmö, Sweden
| | - H Kørner
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
| | - F A Dahl
- Health Services Research Centre, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - T Øresland
- Department of Gastrointestinal Surgery, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - S Yaqub
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - A Papp
- Hudiksvalls Hospital, Hudiksvall
| | - U Ersson
- Hudiksvalls Hospital, Hudiksvall
| | - T Zittel
- Hudiksvalls Hospital, Hudiksvall
| | | | | | - G Dafnis
- Eskilstuna County Hospital, Eskilstuna
| | | | - M Egenvall
- Karolinska University Hospital, Stockholm
| | | | - I Syk
- Skåne University Hospital, Malmö
| | | | - G Arbman
- Vrinnevi Hospital, Linköping University, Norköping
| | - A Chabok
- Västmanland Hospital, Västerås, Norway
| | | | - J Bondi
- Bærum Hospital, Vestre Viken Helseforetak
| | - A Husby
- Diakonhjemmet Hospital, Oslo
| | - R Helander
- Drammen Hospital, Vestre Viken HF, Drammen
| | - A Kjos
- Innlandet Hospital, Hamar
| | | | - A J Talabani
- Levanger Hospital, North-Trøndelag Hospital Trust, Levanger
| | - G Tranø
- Levanger Hospital, North-Trøndelag Hospital Trust, Levanger
| | - I H Nygaard
- Molde Hospital, Helse Møre og Romsdal, Molde
| | | | - O H Sjo
- Oslo University Hospital, Oslo
| | | | | | - M V Gran
- University Hospital of North Norway, Tromsø
| | | | | |
Collapse
|
27
|
Silva CNS, McFarlane SE, Hagen IJ, Rönnegård L, Billing AM, Kvalnes T, Kemppainen P, Rønning B, Ringsby TH, Sæther BE, Qvarnström A, Ellegren H, Jensen H, Husby A. Insights into the genetic architecture of morphological traits in two passerine bird species. Heredity (Edinb) 2017; 119:197-205. [PMID: 28613280 DOI: 10.1038/hdy.2017.29] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/08/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (VP), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of VP). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
Collapse
Affiliation(s)
- C N S Silva
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - S E McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - I J Hagen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - L Rönnegård
- School of Technology and Business Studies, Dalarna University, Falun, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A M Billing
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - P Kemppainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B Rønning
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - T H Ringsby
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - B-E Sæther
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - H Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
28
|
Kemppainen P, Rønning B, Kvalnes T, Hagen IJ, Ringsby TH, Billing AM, Pärn H, Lien S, Husby A, Saether BE, Jensen H. Controlling for P
-value inflation in allele frequency change in experimental evolution and artificial selection experiments. Mol Ecol Resour 2016; 17:770-782. [DOI: 10.1111/1755-0998.12631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Petri Kemppainen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Bernt Rønning
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Ingerid J. Hagen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Thor Harald Ringsby
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Anna M. Billing
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Henrik Pärn
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Sigbjørn Lien
- CIGENE; Norwegian University of Life Sciences; P.O. Box 5003 NO-1432 Ås Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
- Department of Biosciences; University of Helsinki; P.O. Box 65 (Viikinkaari 1) 00014 Helsinki Finland
| | - Bernt-Erik Saether
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| |
Collapse
|
29
|
|
30
|
Husby A, Kawakami T, Rönnegård L, Smeds L, Ellegren H, Qvarnström A. Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait. Proc Biol Sci 2016; 282:20150156. [PMID: 25833857 PMCID: PMC4426624 DOI: 10.1098/rspb.2015.0156] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Understanding the genetic basis of traits involved in adaptation is a major
challenge in evolutionary biology but remains poorly understood. Here, we use
genome-wide association mapping using a custom 50 k single nucleotide
polymorphism (SNP) array in a natural population of collared flycatchers to
examine the genetic basis of clutch size, an important life-history trait in
many animal species. We found evidence for an association on chromosome 18 where
one SNP significant at the genome-wide level explained 3.9% of the
phenotypic variance. We also detected two suggestive quantitative trait loci
(QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were
generally weak and not significant, although there was some indication of a
sex-by-genotype interaction for lifetime reproductive success at the suggestive
QTL on chromosome 26. This implies that sexual antagonism may play a role in
maintaining genetic variation at this QTL. Our findings provide candidate
regions for a classic avian life-history trait that will be useful for future
studies examining the molecular and cellular function of, as well as
evolutionary mechanisms operating at, these loci.
Collapse
Affiliation(s)
- Arild Husby
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway Department of Biosciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Lars Rönnegård
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| |
Collapse
|
31
|
Rönnegård L, McFarlane SE, Husby A, Kawakami T, Ellegren H, Qvarnström A. Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation. Methods Ecol Evol 2016; 7:792-799. [PMID: 27478587 PMCID: PMC4950150 DOI: 10.1111/2041-210x.12535] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/12/2015] [Indexed: 12/03/2022]
Abstract
Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long‐term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single‐nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long‐term study of collared flycatchers in Sweden. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. The method is available in the r package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long‐term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.
Collapse
Affiliation(s)
- Lars Rönnegård
- Department of Clinical Sciences Swedish University of Agricultural Sciences SE-75007 Uppsala Sweden
| | - S Eryn McFarlane
- Department of Animal Ecology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-75236 Uppsala Sweden
| | - Arild Husby
- Department of Biosciences Metapopulation Research Centre University of Helsinki PO Box 65FI-00014 Helsinki Finland; Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology N-7491 Trondheim Norway
| | - Takeshi Kawakami
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-75236 Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-75236 Uppsala Sweden
| | - Anna Qvarnström
- Department of Animal Ecology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-75236 Uppsala Sweden
| |
Collapse
|
32
|
Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H. Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Mol Ecol Resour 2015; 16:727-41. [PMID: 26649993 DOI: 10.1111/1755-0998.12498] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/18/2015] [Accepted: 11/30/2015] [Indexed: 12/24/2022]
Abstract
Dissecting the genetic basis of phenotypic variation in natural populations is a long-standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large-effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 whole-genome-resequenced male collared flycatchers with extreme phenotypes, and on 415 males sampled independent of patch size and genotyped with a 50K SNP chip. No SNPs were genomewide statistically significantly associated with patch size. Simulation-based power analyses suggest that the power to detect large-effect loci responsible for 10% of phenotypic variance was <0.5 in the genome resequencing analysis, and <0.1 in the SNP chip analysis. Reducing the recombination by two-thirds relative to collared flycatchers modestly increased power. Tripling sample size increased power to >0.8 for resequencing of extreme phenotypes (N = 243), but power remained <0.2 for the 50K SNP chip analysis (N = 1245). At least 1 million SNPs were necessary to achieve power >0.8 when analysing 415 randomly sampled phenotypes. However, power of the 50K SNP chip to detect large-effect loci was nearly 0.8 in simulations with a small effective population size of 1500. These results suggest that reliably detecting large-effect trait loci in large natural populations will often require thousands of individuals and near complete sampling of the genome. Encouragingly, far fewer individuals and loci will often be sufficient to reliably detect large-effect loci in small populations with widespread strong linkage disequilibrium.
Collapse
Affiliation(s)
- Marty Kardos
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Arild Husby
- Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, 00014, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - S Eryn McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| |
Collapse
|
33
|
Tringali A, Bowman R, Husby A. Selection and inheritance of sexually dimorphic juvenile plumage coloration. Ecol Evol 2015; 5:5413-5422. [PMID: 30151142 PMCID: PMC6102527 DOI: 10.1002/ece3.1793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/17/2015] [Accepted: 09/28/2015] [Indexed: 11/25/2022] Open
Abstract
Sexually dimorphic plumage coloration is widespread in birds and is generally thought to be a result of sexual selection for more ornamented males. Although many studies find an association between coloration and fitness related traits, few of these simultaneously examine selection and inheritance. Theory predicts that sex‐linked genetic variation can facilitate the evolution of dimorphism, and some empirical work supports this, but we still know very little about the extent of sex linkage of sexually dimorphic traits. We used a longitudinal study on juvenile Florida scrub‐jays (Aphelocoma coerulescens) to estimate strength of selection and autosomal and Z‐linked heritability of mean brightness, UV chroma, and hue. Although plumage coloration signals dominance in juveniles, there was no indication that plumage coloration was related to whether or not an individual bred or its lifetime reproductive success. While mean brightness and UV chroma are moderately heritable, hue is not. There was no evidence for sex‐linked inheritance of any trait with most of the variation explained by maternal effects. The genetic correlation between the sexes was high and not significantly different from unity. These results indicate that evolution of sexual dimorphism in this species is constrained by low sex‐linked heritability and high intersexual genetic correlation.
Collapse
Affiliation(s)
- Angela Tringali
- Avian Ecology Laboratory Archbold Biological Station 123 Main Dr. Venus Florida 33960
| | - Reed Bowman
- Avian Ecology Laboratory Archbold Biological Station 123 Main Dr. Venus Florida 33960
| | - Arild Husby
- Department of Biosciences University of Helsinki PO Box 65 FI-00014 Helsinki Finland
| |
Collapse
|
34
|
Noreikiene K, Herczeg G, Gonda A, Balázs G, Husby A, Merilä J. Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution. Proc Biol Sci 2015; 282:20151008. [PMID: 26108633 PMCID: PMC4590490 DOI: 10.1098/rspb.2015.1008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 11/12/2022] Open
Abstract
The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (Gasterosteus aculeatus). We found that heritabilities were low (average h(2) = 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average rG = 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (rG = 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks.
Collapse
Affiliation(s)
- Kristina Noreikiene
- Ecological Genetics Research Unit, University of Helsinki, Helsinki 00014, Finland
| | - Gábor Herczeg
- Ecological Genetics Research Unit, University of Helsinki, Helsinki 00014, Finland Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest 1117, Hungary
| | - Abigél Gonda
- Ecological Genetics Research Unit, University of Helsinki, Helsinki 00014, Finland
| | - Gergely Balázs
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest 1117, Hungary
| | - Arild Husby
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
35
|
Visser ME, Gienapp P, Husby A, Morrisey M, de la Hera I, Pulido F, Both C. Effects of spring temperatures on the strength of selection on timing of reproduction in a long-distance migratory bird. PLoS Biol 2015; 13:e1002120. [PMID: 25848856 PMCID: PMC4388467 DOI: 10.1371/journal.pbio.1002120] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/03/2015] [Indexed: 11/21/2022] Open
Abstract
Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.
Collapse
Affiliation(s)
- Marcel E. Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arild Husby
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Michael Morrisey
- Dyers Brae House, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Iván de la Hera
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Zoology and Animal Cell Biology, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Francisco Pulido
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid, Spain
| | - Christiaan Both
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Ecology Group, Center for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
36
|
Tsuboi M, Husby A, Kotrschal A, Hayward A, Buechel SD, Zidar J, Løvlie H, Kolm N. Comparative support for the expensive tissue hypothesis: Big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids. Evolution 2014; 69:190-200. [PMID: 25346264 PMCID: PMC4312921 DOI: 10.1111/evo.12556] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/10/2014] [Indexed: 02/06/2023]
Abstract
The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the energetic requirements of encephalization are suggested to impose considerable constraints on brain size evolution. Three main hypotheses concerning how energetic constraints might affect brain evolution predict covariation between brain investment and (1) investment into other costly tissues, (2) overall metabolic rate, and (3) reproductive investment. To date, these hypotheses have mainly been tested in homeothermic animals and the existing data are inconclusive. However, there are good reasons to believe that energetic limitations might play a role in large-scale patterns of brain size evolution also in ectothermic vertebrates. Here, we test these hypotheses in a group of ectothermic vertebrates, the Lake Tanganyika cichlid fishes. After controlling for the effect of shared ancestry and confounding ecological variables, we find a negative association between brain size and gut size. Furthermore, we find that the evolution of a larger brain is accompanied by increased reproductive investment into egg size and parental care. Our results indicate that the energetic costs of encephalization may be an important general factor involved in the evolution of brain size also in ectothermic vertebrates.
Collapse
Affiliation(s)
- Masahito Tsuboi
- Evolutionary Biology Centre, Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Smeds L, Kawakami T, Burri R, Bolivar P, Husby A, Qvarnström A, Uebbing S, Ellegren H. Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes. Nat Commun 2014; 5:5448. [PMID: 25378102 PMCID: PMC4272252 DOI: 10.1038/ncomms6448] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/30/2014] [Indexed: 02/07/2023] Open
Abstract
The molecular characteristics of the pseudoautosomal region (PAR) of sex chromosomes
remain elusive. Despite significant genome-sequencing efforts, the PAR of highly
differentiated avian sex chromosomes remains to be identified. Here we use linkage
analysis together with whole-genome re-sequencing to uncover the 630-kb PAR of an
ecological model species, the collared flycatcher. The PAR contains 22 protein-coding
genes and is GC rich. The genetic length is 64 cM in female meiosis, consistent
with an obligate crossing-over event. Recombination is concentrated to a hotspot region,
with an extreme rate of >700 cM/Mb in a 67-kb segment. We find no signatures
of sexual antagonism and propose that sexual antagonism may have limited influence on
PAR sequences when sex chromosomes are nearly fully differentiated and when a
recombination hotspot region is located close to the PAR boundary. Our results
demonstrate that a very small PAR suffices to ensure homologous recombination and proper
segregation of sex chromosomes during meiosis. The genetic basis of sex chromosome pseudoautosomal regions (PAR) in
organisms with female heterogamety is largely unknown. Smeds et al. provide the
first molecular characterization of the PAR in birds with differentiated sex chromosomes
and show a potential recombination hotspot and no evidence for strong sexual antagonism in
this region.
Collapse
Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Arild Husby
- 1] Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden [2] Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| |
Collapse
|
38
|
|
39
|
Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol Ecol 2014; 23:4035-58. [PMID: 24863701 PMCID: PMC4149781 DOI: 10.1111/mec.12810] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 12/15/2022]
Abstract
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
Collapse
Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H. Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Mol Ecol Resour 2014; 14:1248-60. [PMID: 24784959 PMCID: PMC4368375 DOI: 10.1111/1755-0998.12270] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/14/2014] [Accepted: 04/25/2014] [Indexed: 12/30/2022]
Abstract
With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.
Collapse
Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Schielzeth H, Husby A. Challenges and prospects in genome-wide quantitative trait loci mapping of standing genetic variation in natural populations. Ann N Y Acad Sci 2014; 1320:35-57. [PMID: 24689944 DOI: 10.1111/nyas.12397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A considerable challenge in evolutionary genetics is to understand the genetic mechanisms that facilitate or impede evolutionary adaptation in natural populations. For this, we must understand the genetic loci contributing to trait variation and the selective forces acting on them. The decreased costs and increased feasibility of obtaining genotypic data on a large number of individuals have greatly facilitated gene mapping in natural populations, particularly because organisms whose genetics have been historically difficult to study are now within reach. Here we review the methods available to evolutionary ecologists interested in dissecting the genetic basis of traits in natural populations. Our focus lies on standing genetic variation in outbred populations. We present an overview of the current state of research in the field, covering studies on both plants and animals. We also draw attention to particular challenges associated with the discovery of quantitative trait loci and discuss parallels to studies on crops, livestock, and humans. Finally, we point to some likely future developments in genetic mapping studies.
Collapse
Affiliation(s)
- Holger Schielzeth
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | | |
Collapse
|
42
|
|
43
|
Björklund M, Husby A, Gustafsson L. Rapid and unpredictable changes of the G-matrix in a natural bird population over 25 years. J Evol Biol 2013; 26:1-13. [PMID: 23240615 DOI: 10.1111/jeb.12044] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 08/09/2012] [Accepted: 10/02/2012] [Indexed: 11/30/2022]
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.
Collapse
Affiliation(s)
- M Björklund
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
| | | | | |
Collapse
|
44
|
Rice AM, Vallin N, Kulma K, Arntsen H, Husby A, Tobler M, Qvarnström A. Optimizing the trade-off between offspring number and quality in unpredictable environments: testing the role of differential androgen transfer to collared flycatcher eggs. Horm Behav 2013; 63:813-22. [PMID: 23602767 DOI: 10.1016/j.yhbeh.2013.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 02/28/2013] [Accepted: 03/30/2013] [Indexed: 10/26/2022]
Abstract
According to the brood reduction hypothesis, parents adjust their brood size in response to current environmental conditions. When resources are abundant, parents can successfully raise all hatched offspring, but when resources are scarce, brood reduction, i.e., the sacrifice of some siblings to secure the quality of a subset of offspring, may maximize fitness. Differential transfer of maternal androgens is one potential proximate mechanism through which female birds may facilitate brood reduction because it may alter the relative competitive ability of sibling nestlings. We tested the hypothesis that female collared flycatchers (Ficedula albicollis) manipulate sibling competition by transferring less androgens to eggs late in the laying sequence. We experimentally elevated androgen levels in i) whole clutches and ii) only the two last laid eggs, and compared growth and begging behavior of offspring from these treatments with a control treatment. By using three treatments and video assessment of begging, we examined the effects of within-clutch patterns of yolk androgen transfer on levels of sibling competition in situ. When androgens were elevated in only the two last laid eggs, begging was more even among siblings compared to control nests. We also found that female nestlings receiving additional yolk androgens showed higher mass gain later in the breeding season, while their male counterparts did not. Our results suggest that females may improve reproductive success in unpredictable environments by altering within-clutch patterns of yolk androgen transfer. We discuss the possibility that life-history divergence between the co-occurring collared and pied flycatcher (Ficedula hypoleuca) is amplified by patterns of yolk androgen transfer.
Collapse
Affiliation(s)
- Amber M Rice
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
| | | | | | | | | | | | | |
Collapse
|
45
|
Husby A, Schielzeth H, Forstmeier W, Gustafsson L, Qvarnström A. Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits. Evolution 2012; 67:609-19. [PMID: 23461313 DOI: 10.1111/j.1558-5646.2012.01806.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here, we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex-linked genetic variance (h(2)z ). Of 17 traits examined, eight showed a nonzero h(2)Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak color in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex-linked genetic variance. Sexually selected traits did not show higher h(2)Z than morphological traits and there was only a weak positive relationship between h(2)Z and sexual dimorphism. However, given the relative scarcity of empirical studies, it is premature to make conclusions about the role of sex chromosome linkage in the evolution of sexual dimorphism.
Collapse
Affiliation(s)
- Arild Husby
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
| | | | | | | | | |
Collapse
|
46
|
Affiliation(s)
- A. V. Bushuev
- Department of Vertebrate Zoology Faculty of Biology Lomonosov Moscow State University Moscow Russia
| | - A. Husby
- Department of Animal Ecology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - H. Sternberg
- Ornithologische Arbeitsgemeinschaft für Populationsforschung Braunschweig Braunschweig Germany
| | - V. G. Grinkov
- Evolutionary Biology Department Faculty of Biology Lomonosov Moscow State University Moscow Russia
| |
Collapse
|
47
|
Husby A, Gustafsson L, Qvarnström A. Low Genetic Variance in the Duration of the Incubation Period in a Collared Flycatcher (Ficedula albicollis) Population. Am Nat 2012; 179:132-6. [DOI: 10.1086/663193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
48
|
Vallin N, Rice AM, Bailey RI, Husby A, Qvarnström A. Positive feedback between ecological and reproductive character displacement in a young avian hybrid zone. Evolution 2011; 66:1167-79. [PMID: 22486696 DOI: 10.1111/j.1558-5646.2011.01518.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Character displacement can reduce costly interspecific interactions between young species. We investigated the mechanisms behind divergence in three key traits-breeding habitat choice, timing of breeding, and plumage coloration-in Ficedula flycatchers. We found that male pied flycatchers became expelled from the preferred deciduous habitat into mixed forest as the superior competitor, collared flycatchers, increased in numbers. The peak in food abundance differs between habitats, and the spatial segregation was paralleled by an increased divergence in timing of breeding between the two species. Male pied flycatchers vary from brown to black with brown coloration being more frequent in sympatry with collared flycatchers, a pattern often proposed to result from selection against hybridization, that is, reinforcement. In contrast to this view, we show that brown male pied flycatchers more often hybridize than black males. Male pied flycatcher plumage coloration influenced the territory obtained in areas of co-occurrence with collared flycatchers, and brown male pied flycatchers experienced higher relative fitness than black males when faced with heterospecific competition. We suggest that allopatric divergence in resource defense ability causes a feedback loop at secondary contact where male pied flycatchers with the most divergent strategy compared to collared flycatchers are favored by selection.
Collapse
Affiliation(s)
- Niclas Vallin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | | | | | | | | |
Collapse
|
49
|
Husby A, Hille SM, Visser ME. Testing Mechanisms of Bergmann’s Rule: Phenotypic Decline but No Genetic Change in Body Size in Three Passerine Bird Populations. Am Nat 2011; 178:202-13. [DOI: 10.1086/660834] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
50
|
|