101
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Rice AM, McQuillan MA. Maladaptive learning and memory in hybrids as a reproductive isolating barrier. Proc Biol Sci 2018; 285:20180542. [PMID: 29848649 PMCID: PMC5998094 DOI: 10.1098/rspb.2018.0542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/10/2018] [Indexed: 01/02/2023] Open
Abstract
Selection against hybrid offspring, or postzygotic reproductive isolation, maintains species boundaries in the face of gene flow from hybridization. In this review, we propose that maladaptive learning and memory in hybrids is an important, but overlooked form of postzygotic reproductive isolation. Although a role for learning in premating isolation has been supported, whether learning deficiencies can contribute to postzygotic isolation has rarely been tested. We argue that the novel genetic combinations created by hybridization have the potential to impact learning and memory abilities through multiple possible mechanisms, and that any displacement from optima in these traits is likely to have fitness consequences. We review evidence supporting the potential for hybridization to affect learning and memory, and evidence of links between learning abilities and fitness. Finally, we suggest several avenues for future research. Given the importance of learning for fitness, especially in novel and unpredictable environments, maladaptive learning and memory in hybrids may be an increasingly important source of postzygotic reproductive isolation.
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Affiliation(s)
- Amber M Rice
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Michael A McQuillan
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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102
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Perrier C, Delahaie B, Charmantier A. Heritability estimates from genomewide relatedness matrices in wild populations: Application to a passerine, using a small sample size. Mol Ecol Resour 2018; 18:838-853. [DOI: 10.1111/1755-0998.12886] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 01/16/2023]
Affiliation(s)
- C. Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
| | - B. Delahaie
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
| | - A. Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS‐UMR5175 CEFE Montpellier France
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103
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Kim JM, Santure AW, Barton HJ, Quinn JL, Cole EF, Visser ME, Sheldon BC, Groenen MAM, van Oers K, Slate J. A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol Ecol Resour 2018; 18:877-891. [PMID: 29573186 DOI: 10.1111/1755-0998.12778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/25/2022]
Abstract
High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
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Affiliation(s)
- J-M Kim
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea
| | - A W Santure
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - H J Barton
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
| | - J L Quinn
- School of Biological, Earth and Environmental Science (BEES), University College Cork, Cork, Ireland
| | - E F Cole
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | | | - M E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - B C Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - M A M Groenen
- Wageningen University and Research - Animal Breeding and Genomics, Wageningen, Netherlands
| | - K van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - J Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
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104
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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105
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Guerrero-Bosagna C, Morisson M, Liaubet L, Rodenburg TB, de Haas EN, Košťál Ľ, Pitel F. Transgenerational epigenetic inheritance in birds. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy008. [PMID: 29732172 PMCID: PMC5920295 DOI: 10.1093/eep/dvy008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Elske N de Haas
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Ľubor Košťál
- Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
- Correspondence address. GenPhySE, INRA, 31326 Castanet-Tolosan, France. Tel:+33 561 28 54 35. E-mail:
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106
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da Silva VH, Laine VN, Bosse M, Oers KV, Dibbits B, Visser ME, M A Crooijmans RP, Groenen MAM. CNVs are associated with genomic architecture in a songbird. BMC Genomics 2018; 19:195. [PMID: 29703149 PMCID: PMC6389189 DOI: 10.1186/s12864-018-4577-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/02/2018] [Indexed: 12/11/2022] Open
Abstract
Background Understanding variation in genome structure is essential to understand phenotypic differences within populations and the evolutionary history of species. A promising form of this structural variation is copy number variation (CNV). CNVs can be generated by different recombination mechanisms, such as non-allelic homologous recombination, that rely on specific characteristics of the genome architecture. These structural variants can therefore be more abundant at particular genes ultimately leading to variation in phenotypes under selection. Detailed characterization of CNVs therefore can reveal evolutionary footprints of selection and provide insight in their contribution to phenotypic variation in wild populations. Results Here we use genotypic data from a long-term population of great tits (Parus major), a widely studied passerine bird in ecology and evolution, to detect CNVs and identify genomic features prevailing within these regions. We used allele intensities and frequencies from high-density SNP array data from 2,175 birds. We detected 41,029 CNVs concatenated into 8,008 distinct CNV regions (CNVRs). We successfully validated 93.75% of the CNVs tested by qPCR, which were sampled at different frequencies and sizes. A mother-daughter family structure allowed for the evaluation of the inheritance of a number of these CNVs. Thereby, only CNVs with 40 probes or more display segregation in accordance with Mendelian inheritance, suggesting a high rate of false negative calls for smaller CNVs. As CNVRs are a coarse-grained map of CNV loci, we also inferred the frequency of coincident CNV start and end breakpoints. We observed frequency-dependent enrichment of these breakpoints at homologous regions, CpG sites and AT-rich intervals. A gene ontology enrichment analyses showed that CNVs are enriched in genes underpinning neural, cardiac and ion transport pathways. Conclusion Great tit CNVs are present in almost half of the genes and prominent at repetitive-homologous and regulatory regions. Although overlapping genes under selection, the high number of false negatives make neutrality or association tests on CNVs detected here difficult. Therefore, CNVs should be further addressed in the light of their false negative rate and architecture to improve the comprehension of their association with phenotypes and evolutionary history. Electronic supplementary material The online version of this article (10.1186/s12864-018-4577-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vinicius H da Silva
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands. .,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708PB, The Netherlands.
| | - Veronika N Laine
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands.,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708PB, The Netherlands.,Swedish University of Agricultural Sciences (SLU), Ulls väg 26, Uppsala, 750 07, Sweden
| | - Mirte Bosse
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708PB, The Netherlands
| | - Kees van Oers
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands
| | - Bert Dibbits
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708PB, The Netherlands
| | - Marcel E Visser
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands.,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708PB, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708PB, The Netherlands
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107
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Timm K, Van Oers K, Tilgar V. SERT gene polymorphisms are associated with risk-taking behaviour and breeding parameters in wild great tits. ACTA ACUST UNITED AC 2018; 221:jeb.171595. [PMID: 29361593 DOI: 10.1242/jeb.171595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/03/2018] [Indexed: 11/20/2022]
Abstract
Individual differences in coping with potentially dangerous situations are affected by a combination of genetic and environmental factors. How genetic polymorphisms and behavioural variations are related to fitness is unknown. One of the candidate genes affecting a variety of behavioural processes, including impulsivity, anxiety and mood fluctuations in both humans and other vertebrates, is the serotonin transporter gene (SERT/SLC6A). The aim of this study was to assess an association between SERT genotypes and novelty-seeking and risk-taking behaviours as well as breeding parameters of great tits (Parus major) in a natural environment. We associated polymorphisms in the promoter exonic regions of the SERT gene with parental risk-taking-related behaviour and fitness traits. Our results show that: (1) risk-taking behaviour in our great tit population is linked to single nucleotide polymorphisms in the SERT gene exon 3 and exon 8; (2) the genotype-behaviour associations are consistent with the presence of different stressors; and (3) polymorphisms in exon 8 could be associated with fitness-related traits, such as the start of egg-laying and hatching success. We showed for the first time that genetic variability of SERT plays an important role in shaping individual decision-making that affects fitness in a wild population. However, the results are based on one population and on the polymorphisms that are in a single gene. Therefore, replication studies are needed in order to confirm these preliminary results.
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Affiliation(s)
- Killu Timm
- University of Tartu, Vanemuise 46, Tartu 51101, Estonia
| | - Kees Van Oers
- University of Tartu, Vanemuise 46, Tartu 51101, Estonia
| | - Vallo Tilgar
- University of Tartu, Vanemuise 46, Tartu 51101, Estonia
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108
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Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes. Proc Natl Acad Sci U S A 2018; 115:2794-2799. [PMID: 29483264 PMCID: PMC5856536 DOI: 10.1073/pnas.1717721115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2m version is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2m chromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2m alleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.
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109
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Genomic tools for behavioural ecologists to understand repeatable individual differences in behaviour. Nat Ecol Evol 2018; 2:944-955. [PMID: 29434349 DOI: 10.1038/s41559-017-0411-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 11/10/2017] [Indexed: 12/28/2022]
Abstract
Behaviour is a key interface between an animal's genome and its environment. Repeatable individual differences in behaviour have been extensively documented in animals, but the molecular underpinnings of behavioural variation among individuals within natural populations remain largely unknown. Here, we offer a critical review of when molecular techniques may yield new insights, and we provide specific guidance on how and whether the latest tools available are appropriate given different resources, system and organismal constraints, and experimental designs. Integrating molecular genetic techniques with other strategies to study the proximal causes of behaviour provides opportunities to expand rapidly into new avenues of exploration. Such endeavours will enable us to better understand how repeatable individual differences in behaviour have evolved, how they are expressed and how they can be maintained within natural populations of animals.
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110
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Runemark A, Trier CN, Eroukhmanoff F, Hermansen JS, Matschiner M, Ravinet M, Elgvin TO, Sætre GP. Variation and constraints in hybrid genome formation. Nat Ecol Evol 2018; 2:549-556. [DOI: 10.1038/s41559-017-0437-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022]
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111
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Fang C, Zou C, Fu Y, Li J, Li Y, Ma Y, Zhao S, Li C. DNA methylation changes and evolution of RNA-based duplication in Sus scrofa: based on a two-step strategy. Epigenomics 2018; 10:199-218. [PMID: 29334230 DOI: 10.2217/epi-2017-0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This study aims to couple DNA methylation changes and evolution of retrogenes. MATERIALS & METHODS A new two-step strategy was developed to screen retrogenes. Further, reduced representation bisulfite sequencing and RNA-seq data of eight tissues were used to analyze retrogenes. RESULTS A total of 964 retrocopies were identified and new retrocopies were available for the synthesis of glycans and lipids corresponding to pig phenotypic traits. Retrogenes were consistently hypermethylated. Hypomethylation of parental genes presented more susceptibility to retroposition. Promoter DNA methylation of retrogenes was negatively correlated with evolutionary time and played important roles in regulating retrogene tissue-specific expression pattern. CONCLUSION A two-step procedure is effective and necessary for identifying retrogenes. DNA methylation drives origination, survival, evolution and expression of retrogenes.
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Affiliation(s)
- Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jingxuan Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yunlong Ma
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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112
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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. Recent natural selection causes adaptive evolution of an avian polygenic trait. Science 2018; 358:365-368. [PMID: 29051380 DOI: 10.1126/science.aal3298] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 05/19/2017] [Accepted: 09/12/2017] [Indexed: 12/29/2022]
Abstract
We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
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Affiliation(s)
- Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Wageningen University and Research-Animal Breeding and Genomics, Netherlands
| | - Lewis G Spurgin
- Edward Grey Institute, Department of Zoology, University of Oxford, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, UK
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Ella F Cole
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
| | - Josh A Firth
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Andrew G Gosler
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
| | - Keith McMahon
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
| | - Jocelyn Poissant
- Department of Animal and Plant Sciences, University of Sheffield, UK.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Martien A M Groenen
- Wageningen University and Research-Animal Breeding and Genomics, Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Wageningen University and Research-Animal Breeding and Genomics, Netherlands
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, UK.
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113
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Cheng Y, Gao B, Wang H, Han N, Shao S, Wu S, Song G, Zhang YE, Zhu X, Lu X, Qu Y, Lei F. Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics. Front Zool 2017; 14:58. [PMID: 29299037 PMCID: PMC5740785 DOI: 10.1186/s12983-017-0245-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Beak morphology exhibits considerable adaptive plasticity in birds, which results in highly varied or specialized forms in response to variations in ecology and life history. As the only parid species endemic to the Qinghai-Tibet Plateau, the Ground Tit (Parus humilis) has evolved a distinctly long and curved beak from other parids. An integration of morphometrics, phylogenetics, transcriptomics and embryology allows us to address the evolutionary and developmental mechanisms of the adaptive beak structure observed in the Ground Tit. Results A morphometric approach quantified that the Ground Tit has a comparatively longer and more decurved upper beaks than other parids. We estimated that the ancestor of the Ground Tit likely had a short straight upper beak similar to most current recognized parid species using an ancestral state reconstruction. This morphological specialization is considered an adaptation to its ground-oriented behavior on the high plateau. To identify genetic mechanisms behind this adaptive change, a comparative transcriptomic analysis was applied between the Ground Tit and its closely related species, the Great Tit (Parus major). We detected that 623 genes were significantly differentially expressed in embryonic upper beaks between the two species, 17 of which were functionally annotated to correlate with bone development and morphogenesis, although genes related to bone development were not found to undergo accelerated evolution in the Ground Tit. RT-qPCR validation confirmed differential expression of five out of eight genes that were selected from the 17 genes. Subsequent functional assays in chicken embryos demonstrated that two of these genes, FGF13 and ITGB3, may affect beak morphology by modulating levels of osteoblasts and osteoclasts. Conclusions Our results provide preliminary evidence that development of the long decurved beak of the Ground Tit is likely regulated by transcriptional activities of multiple genes coordinating osteoblasts and osteoclasts. The integration of multiple approaches employed here sheds light on ecological and genetic mechanisms in the evolution of avian morphology.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haitao Wang
- School of Life Sciences, Northeast Normal University, Changchun, 130024 China
| | - Naijian Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shimiao Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shaoyuan Wu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xin Lu
- Department of Ecology, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, 430072 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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Koglin S, Trense D, Wink M, Sauer-Gürth H, Tietze DT. Characterization of a de novo assembled transcriptome of the Common Blackbird ( Turdus merula). PeerJ 2017; 5:e4045. [PMID: 29255646 PMCID: PMC5732540 DOI: 10.7717/peerj.4045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. METHODS Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. RESULTS Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. DISCUSSION Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.
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Affiliation(s)
- Sven Koglin
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Daronja Trense
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Michael Wink
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Hedwig Sauer-Gürth
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Dieter Thomas Tietze
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
- Current affiliation: Natural History Museum Basel, Basel, Switzerland
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116
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Zhang D, Song G, Gao B, Cheng Y, Qu Y, Wu S, Shao S, Wu Y, Alström P, Lei F. Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos). Mol Ecol 2017; 26:6654-6665. [PMID: 29055167 DOI: 10.1111/mec.14383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 11/29/2022]
Abstract
Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions ("genomic differentiation islands") spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene-flow patterns for autosomes using RAD-seq data between two closely related species of long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shaoyuan Wu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shimiao Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yongjie Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Bio-resources and Eco-environment of Ministry of education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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117
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Radersma R, Garroway CJ, Santure AW, de Cauwer I, Farine DR, Slate J, Sheldon BC. Social and spatial effects on genetic variation between foraging flocks in a wild bird population. Mol Ecol 2017; 26:5807-5819. [DOI: 10.1111/mec.14291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 06/29/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Reinder Radersma
- Edward Grey Institute; Department of Zoology; University of Oxford; Oxford UK
- Department of Biology; Lund University; Lund Sweden
| | - Colin J. Garroway
- Edward Grey Institute; Department of Zoology; University of Oxford; Oxford UK
- Department of Biological Sciences; University of Manitoba; Winnipeg MB Canada
| | - Anna W. Santure
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- School of Biological Sciences; The University of Auckland; Auckland New Zealand
| | - Isabelle de Cauwer
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Univ. Lille; CNRS; UMR 8198 - Evo-Eco-Paleo; Lille France
| | - Damien R. Farine
- Edward Grey Institute; Department of Zoology; University of Oxford; Oxford UK
- Department of Collective Behaviour; Max Planck Institute for Ornithology; Konstanz Germany
- Chair of Biodiversity and Collective Behaviour; Department of Biology; University of Konstanz; Konstanz Germany
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Ben C. Sheldon
- Edward Grey Institute; Department of Zoology; University of Oxford; Oxford UK
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118
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Gienapp P, Laine VN, Mateman AC, van Oers K, Visser ME. Environment-Dependent Genotype-Phenotype Associations in Avian Breeding Time. Front Genet 2017; 8:102. [PMID: 28824697 PMCID: PMC5543038 DOI: 10.3389/fgene.2017.00102] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/24/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding how genes shape phenotypes is essential to assess the evolutionary potential of a trait. Identifying the genes underlying quantitative behavioral or life-history traits has, however, proven to be a major challenge. The majority of these traits are phenotypically plastic and different parts of the genome can be involved in shaping the trait under different environmental conditions. These variable genotype-phenotype associations could be one explanation for the limited success of genome-wide association studies in such traits. We here use avian seasonal timing of breeding, a trait that is highly plastic in response to spring temperature, to explore effects of such genotype-by-environment interactions in genome-wide association studies. We genotyped 2045 great tit females for 384081 single nucleotide polymorphisms (SNPs) and recorded their egg-laying dates in the wild. When testing for associations between SNPs and egg-laying dates, no SNP reached genome-wide significance. We then explored whether SNP effects were modified by annual spring temperature by formally testing for an interaction between SNP effect and temperature. The models including the SNP∗temperature interaction performed consistently better although no SNP reached genome-wide significance. Our results suggest that the effects of genes shaping seasonal timing depended on annual spring temperature. Such environment-dependent effects are expected for any phenotypically plastic trait. Taking these effects into account will thus improve the success of detecting genes involved in phenotypically plastic traits, thereby leading to a better understanding of their evolutionary potential.
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Affiliation(s)
- Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - A C Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
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119
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Morand-Ferron J. Why learn? The adaptive value of associative learning in wild populations. Curr Opin Behav Sci 2017. [DOI: 10.1016/j.cobeha.2017.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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120
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Yuan XL, Zhang Z, Li B, Gao N, Zhang H, Sangild PT, Li JQ. Genome-wide DNA methylation analysis of the porcine hypothalamus-pituitary-ovary axis. Sci Rep 2017; 7:4277. [PMID: 28655931 PMCID: PMC5487323 DOI: 10.1038/s41598-017-04603-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Previous studies have suggested that DNA methylation in both CpG and CpH (where H = C, T or A) contexts plays a critical role in biological functions of different tissues. However, the genome-wide DNA methylation patterns of porcine hypothalamus-pituitary-ovary (HPO) tissues remain virtually unexplored. In this study, methylomes of HPO tissues were profiled to investigate their differences and similarities. We found that HPO methylomes displayed tissue-specific methylation patterns in both CpG and CpH contexts. At gene locations, the methylation and density of CpGs was negatively linked at transcription start sites but positively linked at transcription end sites. The densities of CpGs and CpHs at CpG island (CGI) locations were negatively correlated with their methylation. Moreover, the methylation interactions between CGIs and genes showed similar pattern in the CpG context but tissue-specific pattern in the CpH context. CpGs located in CGIs, upstream regions and exons were protected from methylation dynamics, whereas CGI shores, CGI shelves and intergenic regions were more likely to be targets of methylation changes. The methylation dynamics enriching in a tissue-specific manner appeared to maintain and establish the biological functions of HPO tissues. Our analyses provided valuable insights into the tissue-specific methylomes of porcine HPO tissues.
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Affiliation(s)
- Xiao-Long Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Bin Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ning Gao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Sciences, Georg-August University, Albrecht Thaer-Weg 3, Göttingen, Germany
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Per Torp Sangild
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jia-Qi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
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121
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Ghoul M, Andersen SB, West SA. Sociomics: Using Omic Approaches to Understand Social Evolution. Trends Genet 2017; 33:408-419. [PMID: 28506494 DOI: 10.1016/j.tig.2017.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression. This is especially useful in cases where there is clear variation in the level of sociality, such as the social insects. Major tasks for the future are to apply these approaches to a wider range of non-model organisms, and to move from exploratory analyses to the testing of evolutionary theory.
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Affiliation(s)
- Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| | - Sandra B Andersen
- Langone Medical Center, New York University, 423 East 23rd Street, New York, NY 10010, USA.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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122
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Weissensteiner MH, Pang AWC, Bunikis I, Höijer I, Vinnere-Petterson O, Suh A, Wolf JBW. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res 2017; 27:697-708. [PMID: 28360231 PMCID: PMC5411765 DOI: 10.1101/gr.215095.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
| | | | - Ignas Bunikis
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | - Ida Höijer
- SciLife Lab Uppsala, Uppsala University SE-751 85 Uppsala, Sweden
| | | | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
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Peat JR, Ortega-Recalde O, Kardailsky O, Hore TA. The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. F1000Res 2017; 6:526. [PMID: 28580133 PMCID: PMC5437953 DOI: 10.12688/f1000research.11281.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. METHODS We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results: Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. CONCLUSIONS Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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Affiliation(s)
- Julian R Peat
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | | | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
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124
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Transcriptome analysis of a wild bird reveals physiological responses to the urban environment. Sci Rep 2017; 7:44180. [PMID: 28290496 PMCID: PMC5349542 DOI: 10.1038/srep44180] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/06/2017] [Indexed: 12/17/2022] Open
Abstract
Identifying the molecular basis of environmentally induced phenotypic variation presents exciting opportunities for furthering our understanding of how ecological processes and the environment can shape the phenotype. Urban and rural environments present free-living organisms with different challenges and opportunities, which have marked consequences for the phenotype, yet little is known about responses at the molecular level. We characterised transcriptomes from an urban and a rural population of great tits Parus major, demonstrating striking differences in gene expression profiles in both blood and liver tissues. Differentially expressed genes had functions related to immune and inflammatory responses, detoxification, protection against oxidative stress, lipid metabolism, and regulation of gene expression. Many genes linked to stress responses were expressed at higher levels in the urban birds, in accordance with our prediction that urban animals are exposed to greater environmental stress. This is one of the first studies to reveal transcriptional differences between urban- and rural-dwelling animals and suggests an important role for epigenetics in mediating environmentally induced physiological variation. The study provides valuable resources for developing further in-depth studies of the mechanisms driving phenotypic variation in the urban context at larger spatial and temporal scales.
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125
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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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126
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Personality-dependent differences in problem-solving performance in a social context reflect foraging strategies. Behav Processes 2017; 134:95-102. [DOI: 10.1016/j.beproc.2016.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 11/18/2022]
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127
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Romano A, De Giorgio B, Parolini M, Favero C, Possenti CD, Iodice S, Caprioli M, Rubolini D, Ambrosini R, Gianfranceschi L, Saino N, Bollati V. Methylation of the circadian Clock gene in the offspring of a free-living passerine bird increases with maternal and individual exposure to PM 10. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:29-37. [PMID: 27712846 DOI: 10.1016/j.envpol.2016.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/01/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The consequences of exposure to particulate matter (PM) have been thoroughly investigated in humans and other model species, but there is a dearth of studies of the effects of PM on physiology and life-history traits of non-human organisms living in natural or semi-natural environments. Besides toxicological relevance, PM has been recently suggested to exert epigenetic effects by altering DNA methylation patterns. Here, we investigated for the first time the association between the exposure to free-air PM10 and DNA methylation at two loci ('poly-Q exon' and '5'-UTR') of the Clock gene in blood cells of the nestlings of a synanthropic passerine bird, the barn swallow (Hirundo rustica). The Clock gene is a phylogenetically highly conserved gene playing a major role in governing circadian rhythms and circannual life cycles of animals, implying that change in its level of methylation can impact on important fitness traits. We found that methylation at both loci significantly increased with PM10 levels recorded few days before blood sampling, and also with PM10 exposure experienced by the mother during or shortly before egg laying. This study is the first where methylation at a functionally important gene has been shown to vary according to the concentration of anthropogenic pollutants in any animal species in the wild. Since early-life environmental conditions produce epigenetic effects that can transgenerationally be transmitted, DNA methylation of genes controlling photoperiodic response can have far reaching consequences for the ecology and the evolution of wild animal populations.
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Affiliation(s)
- Andrea Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Barbara De Giorgio
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Marco Parolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Chiara Favero
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | | | - Simona Iodice
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Manuela Caprioli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Diego Rubolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences (DISAT), University of Milano Bicocca, Piazza della Scienza, 1, I-20126 Milan, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy.
| | - Nicola Saino
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy.
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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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Schachtschneider KM, Liu Y, Rund LA, Madsen O, Johnson RW, Groenen MAM, Schook LB. Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development. BMC Genomics 2016; 17:856. [PMID: 27809765 PMCID: PMC5094146 DOI: 10.1186/s12864-016-3216-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/26/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Iron deficiency is a common childhood micronutrient deficiency that results in altered hippocampal function and cognitive disorders. However, little is known about the mechanisms through which neonatal iron deficiency results in long lasting alterations in hippocampal gene expression and function. DNA methylation is an epigenetic mark involved in gene regulation and altered by environmental factors. In this study, hippocampal DNA methylation and gene expression were assessed via reduced representation bisulfite sequencing and RNA-seq on samples from a previous study reporting reduced hippocampal-based learning and memory in a porcine biomedical model of neonatal iron deficiency. RESULTS In total 192 differentially expressed genes (DEGs) were identified between the iron deficient and control groups. GO term and pathway enrichment analysis identified DEGs associated with hypoxia, angiogenesis, increased blood brain barrier (BBB) permeability, and altered neurodevelopment and function. Of particular interest are genes previously implicated in cognitive deficits and behavioral disorders in humans and mice, including HTR2A, HTR2C, PAK3, PRSS12, and NETO1. Altered genome-wide DNA methylation was observed across 0.5 million CpG and 2.4 million non-CpG sites. In total 853 differentially methylated (DM) CpG and 99 DM non-CpG sites were identified between groups. Samples clustered by group when comparing DM non-CpG sites, suggesting high conservation of non-CpG methylation in response to neonatal environment. In total 12 DM sites were associated with 9 DEGs, including genes involved in angiogenesis, neurodevelopment, and neuronal function. CONCLUSIONS Neonatal iron deficiency leads to altered hippocampal DNA methylation and gene regulation involved in hypoxia, angiogenesis, increased BBB permeability, and altered neurodevelopment and function. Together, these results provide new insights into the mechanisms through which neonatal iron deficiency results in long lasting reductions in cognitive development in humans.
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Affiliation(s)
- Kyle M. Schachtschneider
- Department of Animal Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, IL 61801 USA
- Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, Wageningen, 6700AH The Netherlands
| | - Yingkai Liu
- Department of Animal Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, IL 61801 USA
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Huimin Road #221, Chengdu, 610000 China
| | - Laurie A. Rund
- Department of Animal Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, IL 61801 USA
| | - Ole Madsen
- Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, Wageningen, 6700AH The Netherlands
| | - Rodney W. Johnson
- Department of Animal Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, IL 61801 USA
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, Wageningen, 6700AH The Netherlands
| | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, IL 61801 USA
- Institute for Genomic Biology, University of Illinois, 1206 W Gregory Drive, Urbana, IL 61801 USA
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130
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Moiron M, Mathot KJ, Dingemanse NJ. A multi-level approach to quantify speed-accuracy trade-offs in great tits (Parus major). Behav Ecol 2016. [DOI: 10.1093/beheco/arw077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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131
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Derks MFL, Schachtschneider KM, Madsen O, Schijlen E, Verhoeven KJF, van Oers K. Gene and transposable element methylation in great tit (Parus major) brain and blood. BMC Genomics 2016; 17:332. [PMID: 27146629 PMCID: PMC4855439 DOI: 10.1186/s12864-016-2653-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/22/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological model species, the great tit (Parus major). RESULTS We show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for CGI methylation in regulating expression during development. Additionally, we find significant non-CpG methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally, CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated with TE expression. CONCLUSION The discovery that TSS methylation levels are directly linked to functional classes related to each tissue provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory form of methylation in TE silencing.
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Affiliation(s)
- Martijn F L Derks
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Kyle M Schachtschneider
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, USA
| | - Ole Madsen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Elio Schijlen
- PRI Bioscience, Plant Research International, Wageningen UR, Wageningen, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial 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.
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132
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Verhulst EC, Mateman AC, Zwier MV, Caro SP, Verhoeven KJF, van Oers K. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation. Mol Ecol 2016; 25:1801-11. [PMID: 26678756 DOI: 10.1111/mec.13519] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022]
Abstract
Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency.
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Affiliation(s)
- Eveline C Verhulst
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - A Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Mathijs V Zwier
- Center for Liver, Digestive and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, P.O. Box 196, 9700 AD, Groningen, The Netherlands
| | - Samuel P Caro
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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