1
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Brand JA, Garcia-Gonzalez F, Dowling DK, Wong BBM. Mitochondrial genetic variation as a potential mediator of intraspecific behavioural diversity. Trends Ecol Evol 2024; 39:199-212. [PMID: 37839905 DOI: 10.1016/j.tree.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
Mitochondrial genes play an essential role in energy metabolism. Variation in the mitochondrial DNA (mtDNA) sequence often exists within species, and this variation can have consequences for energy production and organismal life history. Yet, despite potential links between energy metabolism and the expression of animal behaviour, mtDNA variation has been largely neglected to date in studies investigating intraspecific behavioural diversity. We outline how mtDNA variation and interactions between mitochondrial and nuclear genotypes may contribute to the expression of individual-to-individual behavioural differences within populations, and why such effects may lead to sex differences in behaviour. We contend that integration of the mitochondrial genome into behavioural ecology research may be key to fully understanding the evolutionary genetics of animal behaviour.
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Affiliation(s)
- Jack A Brand
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia; Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Francisco Garcia-Gonzalez
- Doñana Biological Station-CSIC, Seville, Spain; Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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2
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Balog K, Mizeranschi AE, Wanjala G, Sipos B, Kusza S, Bagi Z. Application potential of chicken DNA chip in domestic pigeon species - Preliminary results. Saudi J Biol Sci 2023; 30:103594. [PMID: 36874200 PMCID: PMC9975693 DOI: 10.1016/j.sjbs.2023.103594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.
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Affiliation(s)
- Katalin Balog
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | | | - George Wanjala
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Bíborka Sipos
- University of Debrecen, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi út 138, 4032, Debrecen, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
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3
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Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs. CONSERV GENET RESOUR 2022; 14:203-213. [PMID: 35673611 PMCID: PMC9162989 DOI: 10.1007/s12686-022-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.
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4
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Sun TH, Shao YHJ, Mao CL, Hung MN, Lo YY, Ko TM, Hsiao TH. A Novel Quality-Control Procedure to Improve the Accuracy of Rare Variant Calling in SNP Arrays. Front Genet 2021; 12:736390. [PMID: 34764980 PMCID: PMC8577504 DOI: 10.3389/fgene.2021.736390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Single-nucleotide polymorphism (SNP) arrays are an ideal technology for genotyping genetic variants in mass screening. However, using SNP arrays to detect rare variants [with a minor allele frequency (MAF) of <1%] is still a challenge because of noise signals and batch effects. An approach that improves the genotyping quality is needed for clinical applications. Methods: We developed a quality-control procedure for rare variants which integrates different algorithms, filters, and experiments to increase the accuracy of variant calling. Using data from the TWB 2.0 custom Axiom array, we adopted an advanced normalization adjustment to prevent false calls caused by splitting the cluster and a rare het adjustment which decreases false calls in rare variants. The concordance of allelic frequencies from array data was compared to those from sequencing datasets of Taiwanese. Finally, genotyping results were used to detect familial hypercholesterolemia (FH), thrombophilia (TH), and maturity-onset diabetes of the young (MODY) to assess the performance in disease screening. All heterozygous calls were verified by Sanger sequencing or qPCR. The positive predictive value (PPV) of each step was estimated to evaluate the performance of our procedure. Results: We analyzed SNP array data from 43,433 individuals, which interrogated 267,247 rare variants. The advanced normalization and rare het adjustment methods adjusted genotyping calling of 168,134 variants (96.49%). We further removed 3916 probesets which were discordant in MAFs between the SNP array and sequencing data. The PPV for detecting pathogenic variants with 0.01%10,000 are available. The results demonstrated our procedure could perform correct genotype calling of rare variants. It provides a solution of pathogenic variant detection through SNP array. The approach brings tremendous promise for implementing precision medicine in medical practice.
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Affiliation(s)
- Ting-Hsuan Sun
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Hsuan Joni Shao
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chien-Lin Mao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Miao-Neng Hung
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yi-Yun Lo
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Research Center for Biomedical Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan
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5
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Lindner M, Gawehns F, Te Molder S, Visser ME, van Oers K, Laine VN. Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species. Mol Ecol Resour 2021; 22:834-846. [PMID: 34435438 PMCID: PMC9290141 DOI: 10.1111/1755-0998.13493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/17/2022]
Abstract
The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulphite sequencing is commonly used for assessing genome‐wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulphite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non‐model species, which often lack genomic references. Here, we used whole‐genome bisulphite sequencing (WGBS) data from four female great tits (Parus major) to evaluate the performance of seven tools for SNP calling from bisulphite sequencing data. We used SNPs from whole‐genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (bis‐snp), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.
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Affiliation(s)
- Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Fleur Gawehns
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Sebastiaan Te Molder
- 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.,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
| | - 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
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6
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Lee KD, Millar CD, Brekke P, Whibley A, Ewen JG, Hingston M, Zhu A, Santure AW. The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi. Mol Ecol Resour 2021; 22:415-429. [PMID: 34323011 DOI: 10.1111/1755-0998.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.
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Affiliation(s)
- Kate D Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Melanie Hingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Amy Zhu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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7
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Henriques D, Lopes AR, Chejanovsky N, Dalmon A, Higes M, Jabal-Uriel C, Le Conte Y, Reyes-Carreño M, Soroker V, Martín-Hernández R, Pinto MA. A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.). Sci Rep 2021; 11:15317. [PMID: 34321557 PMCID: PMC8319136 DOI: 10.1038/s41598-021-94833-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3' and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.
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Affiliation(s)
- Dora Henriques
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Ana R Lopes
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Nor Chejanovsky
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Anne Dalmon
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | - Mariano Higes
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Clara Jabal-Uriel
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
| | - Yves Le Conte
- INRAE, Unité Abeilles et Environnement, Avignon, France
| | | | - Victoria Soroker
- Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Raquel Martín-Hernández
- IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología (INCRECYT-FEDER), Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - M Alice Pinto
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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8
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Salmón P, Jacobs A, Ahrén D, Biard C, Dingemanse NJ, Dominoni DM, Helm B, Lundberg M, Senar JC, Sprau P, Visser ME, Isaksson C. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat Commun 2021; 12:2983. [PMID: 34016968 PMCID: PMC8137928 DOI: 10.1038/s41467-021-23027-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 04/01/2021] [Indexed: 02/03/2023] Open
Abstract
Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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Affiliation(s)
- Pablo Salmón
- Department of Biology, Lund University, Lund, Sweden.
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Dag Ahrén
- Department of Biology, Lund University, Lund, Sweden
| | - Clotilde Biard
- Sorbonne Université, UPEC, Paris 7, CNRS, INRA, IRD, Institut d'Écologie et des Sciences de l'Environnement de Paris, iEES Paris, F-75005, Paris, France
| | - Niels J Dingemanse
- Department of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Davide M Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Barbara Helm
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | | | - Philipp Sprau
- Department of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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9
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De-Kayne R, Frei D, Greenway R, Mendes SL, Retel C, Feulner PGD. Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets. Mol Ecol Resour 2020; 21:653-660. [PMID: 33314612 DOI: 10.1111/1755-0998.13309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022]
Abstract
Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic data sets in an increasing number of nonmodel species. Additionally, these new data provide the opportunity for combining data sets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher throughput of data at a lower per-base cost, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four-channel system to a two-channel system. We caution that when data are combined from these two systems, erroneous guanine base calls that result from the two-channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artefacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever-changing sequencing platform technology.
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Affiliation(s)
- Rishi De-Kayne
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Frei
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ryan Greenway
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Sofia L Mendes
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Cas Retel
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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10
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van Oers K, Sepers B, Sies W, Gawehns F, Verhoeven KJF, Laine VN. Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird. Integr Comp Biol 2020; 60:1517-1530. [PMID: 33031487 PMCID: PMC7742756 DOI: 10.1093/icb/icaa138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.
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Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research, Wageningen, P.O. Box 338, 6700 AH, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research, Wageningen, P.O. Box 338, 6700 AH, the Netherlands
| | - William Sies
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Fleur Gawehns
- Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
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11
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Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
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Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
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12
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Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, Santure AW. Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta). Proc Biol Sci 2020; 287:20200948. [PMID: 32842928 PMCID: PMC7482260 DOI: 10.1098/rspb.2020.0948] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head-bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head-bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Kate D. Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - John G. Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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13
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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14
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Jones JC, Du ZG, Bernstein R, Meyer M, Hoppe A, Schilling E, Ableitner M, Juling K, Dick R, Strauss AS, Bienefeld K. Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee. Ecol Evol 2020; 10:6246-6256. [PMID: 32724511 PMCID: PMC7381592 DOI: 10.1002/ece3.6357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023] Open
Abstract
High-throughput high-density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here, we have developed a new high-density SNP genotyping array (103,270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole-genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behavior against pathogens, foraging, and subspecies. Additionally, markers from a GWAS of hygienic behavior against the major honey bee parasite Varroa destructor were brought over. The chip also includes SNPs associated with each of three major breeding objectives-honey yield, gentleness, and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by nonlethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation, and conservation questions.
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Affiliation(s)
- Julia C. Jones
- Institute for Bee ResearchHohen NeuendorfGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Zhipei G. Du
- Institute for Bee ResearchHohen NeuendorfGermany
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15
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Gienapp P. Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change? GLOBAL CHANGE BIOLOGY 2020; 26:2737-2749. [PMID: 32108978 DOI: 10.1111/gcb.15058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 05/22/2023]
Abstract
Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the 'evolutionary potential' of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high-throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene-mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.
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16
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Verhagen I, Tomotani BM, Gienapp P, Visser ME. Temperature has a causal and plastic effect on timing of breeding in a small songbird. J Exp Biol 2020; 223:jeb218784. [PMID: 32205357 DOI: 10.1242/jeb.218784] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/17/2020] [Indexed: 12/21/2022]
Abstract
Phenotypic plasticity is an important mechanism by which an individual can adapt its seasonal timing to predictable, short-term environmental changes by using predictive cues. Identification of these cues is crucial to forecast the response of species to long-term environmental change and to study their potential to adapt. Individual great tits (Parus major) start reproduction early under warmer conditions in the wild, but whether this effect is causal is not well known. We housed 36 pairs of great tits in climate-controlled aviaries and 40 pairs in outdoor aviaries, where they bred under artificial contrasting temperature treatments or in semi-natural conditions, respectively, for two consecutive years, using birds from lines selected for early and late egg laying. We thus obtained laying dates in two different thermal environments for each female. Females bred earlier under warmer conditions in climate-controlled aviaries, but not in outdoor aviaries. The latter was inconsistent with laying dates from our wild population. Further, early selection line females initiated egg laying consistently ∼9 days earlier than late selection line females in outdoor aviaries, but we found no difference in the degree of plasticity (i.e. the sensitivity to temperature) in laying date between selection lines. Because we found that temperature causally affects laying date, climate change will lead to earlier laying. This advancement is, however, unlikely to be sufficient, thereby leading to selection for earlier laying. Our results suggest that natural selection may lead to a change in mean phenotype, but not to a change in the sensitivity of laying dates to temperature.
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Affiliation(s)
- Irene Verhagen
- Department of Animal Ecology, Netherland Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Barbara M Tomotani
- Department of Animal Ecology, Netherland Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Phillip Gienapp
- Department of Animal Ecology, Netherland Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherland Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
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17
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da Silva VH, Laine VN, Bosse M, Spurgin LG, Derks MFL, van Oers K, Dibbits B, Slate J, Crooijmans RPMA, Visser ME, Groenen MAM. The Genomic Complexity of a Large Inversion in Great Tits. Genome Biol Evol 2020; 11:1870-1881. [PMID: 31114855 PMCID: PMC6609730 DOI: 10.1093/gbe/evz106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosome inversions have clear effects on genome evolution and have been associated with speciation, adaptation, and the evolution of the sex chromosomes. In birds, these inversions may play an important role in hybridization of species and disassortative mating. We identified a large (≈64 Mb) inversion polymorphism in the great tit (Parus major) that encompasses almost 1,000 genes and more than 90% of Chromosome 1A. The inversion occurs at a low frequency in a set of over 2,300 genotyped great tits in the Netherlands with only 5% of the birds being heterozygous for the inversion. In an additional analysis of 29 resequenced birds from across Europe, we found two heterozygotes. The likely inversion breakpoints show considerable genomic complexity, including multiple copy number variable segments. We identified different haplotypes for the inversion, which differ in the degree of recombination in the center of the chromosome. Overall, this remarkable genetic variant is widespread among distinct great tit populations and future studies of the inversion haplotype, including how it affects the fitness of carriers, may help to understand the mechanisms that maintain it.
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Affiliation(s)
- Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Veronika N Laine
- Department of Molecular and Cellular Biology, Harvard University
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park University of East Anglia, Norwich, United Kingdom
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Jon Slate
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom
| | | | - Marcel E Visser
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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18
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Verhagen I, Laine VN, Mateman AC, Pijl A, de Wit R, van Lith B, Kamphuis W, Viitaniemi HM, Williams TD, Caro SP, Meddle SL, Gienapp P, van Oers K, Visser ME. Fine-tuning of seasonal timing of breeding is regulated downstream in the underlying neuro-endocrine system in a small songbird. ACTA ACUST UNITED AC 2019; 222:jeb.202481. [PMID: 31371403 DOI: 10.1242/jeb.202481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022]
Abstract
The timing of breeding is under selection in wild populations as a result of climate change, and understanding the underlying physiological processes mediating this timing provides insight into the potential rate of adaptation. Current knowledge on this variation in physiology is, however, mostly limited to males. We assessed whether individual differences in the timing of breeding in females are reflected in differences in candidate gene expression and, if so, whether these differences occur in the upstream (hypothalamus) or downstream (ovary and liver) parts of the neuroendocrine system. We used 72 female great tits from two generations of lines artificially selected for early and late egg laying, which were housed in climate-controlled aviaries and went through two breeding cycles within 1 year. In the first breeding season we obtained individual egg-laying dates, while in the second breeding season, using the same individuals, we sampled several tissues at three time points based on the timing of the first breeding attempt. For each tissue, mRNA expression levels were measured using qPCR for a set of candidate genes associated with the timing of reproduction and subsequently analysed for differences between generations, time points and individual timing of breeding. We found differences in gene expression between generations in all tissues, with the most pronounced differences in the hypothalamus. Differences between time points, and early- and late-laying females, were found exclusively in the ovary and liver. Altogether, we show that fine-tuning of the seasonal timing of breeding, and thereby the opportunity for adaptation in the neuroendocrine system, is regulated mostly downstream in the neuro-endocrine system.
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Affiliation(s)
- Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - A Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Agata Pijl
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Ruben de Wit
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Bart van Lith
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Willem Kamphuis
- Netherlands Institute for Neuroscience (NIN-KNAW), 1105 BA Amsterdam-Zuidoost, The Netherlands
| | - Heidi M Viitaniemi
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Tony D Williams
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Samuel P Caro
- Departement d'Ecologie Evolutive, Centre d'Ecologie Fonctionnelle & Evolutive, 34293 Montpellier 5, France
| | - Simone L Meddle
- Department of Behavioural Neuroendocrinology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
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19
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Laine VN, Verhagen I, Mateman AC, Pijl A, Williams TD, Gienapp P, van Oers K, Visser ME. Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird. BMC Genomics 2019; 20:693. [PMID: 31477015 PMCID: PMC6720064 DOI: 10.1186/s12864-019-6043-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression. RESULTS Birds from the selection lines differed in expression especially for one gene with clear reproductive functions, zona pellucida glycoprotein 4 (ZP4), which has also been shown to be under selection in these lines. Genes were differentially expressed at different time points in all tissues and most of the differentially expressed genes between the two temperature treatments were found in the liver. We identified a set of hub genes from all the tissues which showed high association to hormonal functions, suggesting that they have a core function in timing of breeding. We also found ample differentially expressed genes with largely unknown functions in birds. CONCLUSIONS We found differentially expressed genes associated with selection line and temperature treatment. Interestingly, the latter mainly in the liver suggesting that temperature effects on egg-laying date may happen down-stream in the physiological pathway. These findings, as well as our datasets, will further the knowledge of the mechanisms of tissue-specific avian seasonality in the future.
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Affiliation(s)
- Veronika N. Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - A. Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Agata Pijl
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Tony D. Williams
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
| | - Marcel E. Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
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20
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Verhagen I, Gienapp P, Laine VN, Grevenhof EM, Mateman AC, Oers K, Visser ME. Genetic and phenotypic responses to genomic selection for timing of breeding in a wild songbird. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Irene Verhagen
- 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
| | - Veronika N. Laine
- Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Elizabeth M. Grevenhof
- Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Andrea C. Mateman
- Department of Animal Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Kees Oers
- 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
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21
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Bosse M, Spurgin LG, Laine VN, Cole EF, Firth JA, Gienapp P, Gosler AG, McMahon K, Poissant J, Verhagen I, Groenen MAM, van Oers K, Sheldon BC, Visser ME, Slate J. Response to Perrier and Charmantier: On the importance of time scales when studying adaptive evolution. Evol Lett 2019; 3:248-253. [PMID: 31171980 PMCID: PMC6546378 DOI: 10.1002/evl3.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/13/2019] [Indexed: 11/26/2022] Open
Affiliation(s)
- Mirte Bosse
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Lewis G. Spurgin
- School of Biological SciencesUniversity of East AngliaUnited Kingdom
| | - Veronika N. Laine
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Ella F. Cole
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Josh A. Firth
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Phillip Gienapp
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Andrew G. Gosler
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Keith McMahon
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary MedicineUniversity of CalgaryCanada
| | - Irene Verhagen
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Martien A. M. Groenen
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Ben C. Sheldon
- Edward Grey Institute, Department of ZoologyUniversity of OxfordUnited Kingdom
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Wageningen University and Research—Animal Breeding and GenomicsWageningenThe Netherlands
| | - Jon Slate
- Department of Animal and Plant SciencesUniversity of SheffieldUnited Kingdom
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22
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Laine VN, Atema E, Vlaming P, Verhagen I, Mateman C, Ramakers JJC, van Oers K, Spoelstra K, Visser ME. The Genomics of Circadian Timing in a Wild Bird, the Great Tit (Parus major). Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Gienapp P, Calus MPL, Laine VN, Visser ME. Genomic selection on breeding time in a wild bird population. Evol Lett 2019; 3:142-151. [PMID: 31289689 PMCID: PMC6591552 DOI: 10.1002/evl3.103] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Artificial selection experiments are a powerful tool in evolutionary biology. Selecting individuals based on multimarker genotypes (genomic selection) has several advantages over phenotype-based selection but has, so far, seen very limited use outside animal and plant breeding. Genomic selection depends on the markers tagging the causal loci that underlie the selected trait. Because the number of necessary markers depends, among other factors, on effective population size, genomic selection may be in practice not feasible in wild populations as most wild populations have much higher effective population sizes than domesticated populations. However, the current possibilities of cost-effective high-throughput genotyping could overcome this limitation and thereby make it possible to apply genomic selection also in wild populations. Using a unique dataset of about 2000 wild great tits (Parus major), a small passerine bird, genotyped on a 650 k SNP chip we calculated genomic breeding values for egg-laying date using the so-called GBLUP approach. In this approach, the pedigree-based relatedness matrix of an "animal model," a special form of the mixed model, is replaced by a marker-based relatedness matrix. Using the marker-based relatedness matrix, the model seemed better able to disentangle genetic and permanent environmental effects. We calculated the accuracy of genomic breeding values by correlating them to the phenotypes of individuals whose phenotypes were excluded from the analysis when estimating the genomic breeding values. The obtained accuracy was about 0.20, with very little effect of the used genomic relatedness estimator but a strong effect of the number of SNPs. The obtained accuracy is lower than typically seen in domesticated species but considerable for a trait with low heritability (∼0.2) as avian breeding time. Our results show that genomic selection is possible also in wild populations with potentially many applications, which we discuss here.
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Affiliation(s)
- Phillip Gienapp
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Mario P. L. Calus
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Veronika N. Laine
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
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Laine VN, Gossmann TI, van Oers K, Visser ME, Groenen MAM. Exploring the unmapped DNA and RNA reads in a songbird genome. BMC Genomics 2019; 20:19. [PMID: 30621573 PMCID: PMC6323668 DOI: 10.1186/s12864-018-5378-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/16/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence. RESULTS Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma. CONCLUSIONS Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.
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Affiliation(s)
- Veronika N Laine
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands.
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK
| | - Kees van Oers
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands.,Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Martien A M Groenen
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
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Santure AW, Garant D. Wild GWAS-association mapping in natural populations. Mol Ecol Resour 2018; 18:729-738. [PMID: 29782705 DOI: 10.1111/1755-0998.12901] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/27/2022]
Abstract
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such "gene mapping" studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment. These studies are also allowing us to gain insight into the evolutionary processes maintaining variation in natural populations, to better understand genotype-by-environment and epistatic interactions and to track the dynamics of allele frequency change at loci contributing to traits under selection. Gene mapping in the wild using genomewide association scans (GWAS) do, however, come with a number of methodological challenges, not least the population structure in space and time inherent to natural populations. We here provide an overview of these challenges, summarize the exciting methodological advances and applications of association mapping in natural populations reported in this special issue and provide some guidelines for future "wild GWAS" research.
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Affiliation(s)
- Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Dany Garant
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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