101
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Leaché AD, Oaks JR. The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022645] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Adam D. Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington 98195
| | - Jamie R. Oaks
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849
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102
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Wang M, Uebbing S, Ellegren H. Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations. Genome Biol Evol 2017; 9:1266-1279. [PMID: 28453623 PMCID: PMC5434935 DOI: 10.1093/gbe/evx080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximizes data usage by borrowing information from the whole data set and combines several SNPs per transcript to detect ASE. Of 2,576 transcripts analyzed in collared flycatcher, ASE was detected in 185 (7.2%) and a similar frequency was seen in the pied flycatcher. Transcripts with statistically significant ASE commonly showed the major allele in >90% of the reads, reflecting that power was highest when expression was heavily biased toward one of the alleles. This would suggest that the observed frequencies of ASE likely are underestimates. The proportion of ASE transcripts varied among tissues, being lowest in testis and highest in muscle. Individuals often showed ASE of particular transcripts in more than one tissue (73.4%), consistent with a genetic basis for regulation of gene expression. The results suggest that genetic variation in regulatory sequences commonly affects gene expression in natural populations and that it provides a seedbed for phenotypic evolution via divergence in gene expression.
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Affiliation(s)
- Mi Wang
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
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103
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Chromosomal inversion differences correlate with range overlap in passerine birds. Nat Ecol Evol 2017; 1:1526-1534. [PMID: 29185507 DOI: 10.1038/s41559-017-0284-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/19/2017] [Indexed: 11/08/2022]
Abstract
Chromosomal inversions evolve frequently but the reasons for this remain unclear. We used cytological descriptions of 411 species of passerine birds to identify large pericentric inversion differences between species, based on the position of the centromere. Within 81 small clades comprising 284 of the species, we found 319 differences on the 9 largest autosomes combined, 56 on the Z chromosome, and 55 on the W chromosome. We also identified inversions present within 32 species. Using a new fossil-calibrated phylogeny, we examined the phylogenetic, demographic and genomic context in which these inversions have evolved. The number of inversion differences between closely related species is consistently predicted by whether the ranges of species overlap, even when time is controlled for as far as is possible. Fixation rates vary across the autosomes, but inversions are more likely to be fixed on the Z chromosome than the average autosome. Variable mutagenic input alone (estimated by chromosome size, map length, GC content or repeat density) cannot explain the differences between chromosomes in the number of inversions fixed. Together, these results support a model in which inversions increase because of their effects on recombination suppression in the face of hybridization. Other factors associated with hybridization may also contribute, including the possibility that inversions contain incompatibility alleles, making taxa less likely to collapse following secondary contact.
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104
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Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 2017; 30:1450-1477. [DOI: 10.1111/jeb.13047] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Affiliation(s)
- M. Ravinet
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; Oslo Norway
- National Institute of Genetics; Mishima Shizuoka Japan
| | - R. Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado; Universidade do Porto; Vairão Portugal
- Department of Experimental and Health Sciences; IBE, Institute of Evolutionary Biology (CSIC-UPF); Pompeu Fabra University; Barcelona Spain
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Marine Sciences; Centre for Marine Evolutionary Biology; University of Gothenburg; Gothenburg Sweden
| | - J. Galindo
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Vigo Spain
| | - N. Bierne
- CNRS; Université Montpellier; ISEM; Station Marine Sète France
| | - M. Rafajlović
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | | | - B. Mehlig
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | - A. M. Westram
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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105
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Johnston SE, Huisman J, Ellis PA, Pemberton JM. A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer ( Cervus elaphus). G3 (BETHESDA, MD.) 2017; 7:2859-2870. [PMID: 28667018 PMCID: PMC5555489 DOI: 10.1534/g3.117.044198] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
Abstract
High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion, and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7 cM and the genome-wide autosomal recombination rate was 1.04 cM/Mb. The female autosomal map length was 1.21 longer than that of males (2767.4 cM vs. 2280.8 cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement, and population management in red deer and related species.
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Affiliation(s)
- Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Jisca Huisman
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
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106
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Burri R. Interpreting differentiation landscapes in the light of long-term linked selection. Evol Lett 2017. [DOI: 10.1002/evl3.14] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Reto Burri
- Department of Population Ecology; Friedrich Schiller University Jena; Dornburger Strasse 159 D-07743 Jena Germany
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107
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Kawakami T, Mugal CF, Suh A, Nater A, Burri R, Smeds L, Ellegren H. Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds. Mol Ecol 2017; 26:4158-4172. [DOI: 10.1111/mec.14197] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/02/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
| | - Alexander Suh
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
| | - Alexander Nater
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zürich Switzerland
| | - Reto Burri
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
- Department of Population Ecology; Friedrich Schiller University Jena; Jena Germany
| | - Linnéa Smeds
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre (EBC); Uppsala University; Uppsala Sweden
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108
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Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation. G3-GENES GENOMES GENETICS 2017; 7:2115-2124. [PMID: 28500054 PMCID: PMC5499121 DOI: 10.1534/g3.117.041178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.
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109
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Vijay N, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW. Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Mol Ecol 2017; 26:4284-4295. [PMID: 28570015 DOI: 10.1111/mec.14195] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 12/15/2022]
Abstract
Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.
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Affiliation(s)
- Nagarjun Vijay
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Lab of Molecular and Genomic Evolution, Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Weissensteiner
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Reto Burri
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Takeshi Kawakami
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hans Ellegren
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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110
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Butler JB, Vaillancourt RE, Potts BM, Lee DJ, King GJ, Baten A, Shepherd M, Freeman JS. Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement. BMC Genomics 2017; 18:397. [PMID: 28532390 PMCID: PMC5441008 DOI: 10.1186/s12864-017-3782-7] [Citation(s) in RCA: 14] [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: 08/09/2016] [Accepted: 05/10/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. RESULTS We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. CONCLUSIONS These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.
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Affiliation(s)
- J B Butler
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - R E Vaillancourt
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - B M Potts
- School of Biological Science and ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - D J Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD, 4558, Australia
| | - G J King
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - A Baten
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - M Shepherd
- Southern Cross Plant Science, Southern Cross University, Military Rd, Lismore, NSW, 2480, Australia
| | - J S Freeman
- School of Biological Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
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111
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Andersen MJ, Manthey JD, Naikatini A, Moyle RG. Conservation genomics of the silktail (Aves: Lamprolia victoriae) suggests the need for increased protection of native forest on the Natewa Peninsula, Fiji. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0979-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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112
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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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113
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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114
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Van Doren BM, Campagna L, Helm B, Illera JC, Lovette IJ, Liedvogel M. Correlated patterns of genetic diversity and differentiation across an avian family. Mol Ecol 2017; 26:3982-3997. [PMID: 28256062 DOI: 10.1111/mec.14083] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/01/2023]
Abstract
Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation.
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Affiliation(s)
- Benjamin M Van Doren
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Leonardo Campagna
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Barbara Helm
- Animal Health and Comparative Medicine, Institute of Biodiversity, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Campus of Mieres, Research Building, 5th Floor, c/ Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Miriam Liedvogel
- Max Planck Institute for Evolutionary Biology, AG Behavioural Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany
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115
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Shipilina D, Serbyn M, Ivanitskii V, Marova I, Backström N. Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff ( Phylloscopus collybita abietinus/tristis) hybrid zone. Ecol Evol 2017; 7:2169-2180. [PMID: 28405281 PMCID: PMC5383471 DOI: 10.1002/ece3.2782] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022] Open
Abstract
Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole‐genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region—the previously described subspecies (“fulvescens”) from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.
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Affiliation(s)
- Daria Shipilina
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Maksym Serbyn
- Department of Physics University of California Berkeley CA USA
| | - Vladimir Ivanitskii
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Irina Marova
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Niclas Backström
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
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116
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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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117
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Dutoit L, Vijay N, Mugal CF, Bossu CM, Burri R, Wolf J, Ellegren H. Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Proc Biol Sci 2017; 284:20162756. [PMID: 28202815 PMCID: PMC5326536 DOI: 10.1098/rspb.2016.2756] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/18/2017] [Indexed: 12/30/2022] Open
Abstract
Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's ρ = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.
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Affiliation(s)
- Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Nagarjun Vijay
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Christen M Bossu
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Jochen Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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118
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Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences. Genetics 2017; 205:1319-1334. [PMID: 28100590 DOI: 10.1534/genetics.116.198861] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/11/2017] [Indexed: 01/25/2023] Open
Abstract
Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287 Ficedula flycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate. However, this pattern was substantially weaker when ROH were mapped using genetic rather than physical single nucleotide polymorphism (SNP) coordinates in the genome. Empirical results and simulations suggest that high ROH abundance in regions of low recombination was partly caused by increased power to detect the very long IBD segments typical of regions with a low recombination rate. Simulations also showed that hard selective sweeps (but not soft sweeps or background selection) likely contributed to variation in the abundance of ROH across the genome. Comparisons of the abundance of ROH among several study populations indicated that the Spanish pied flycatcher population had the smallest historical effective population size (Ne) for this species, and that a putatively recently founded island (Baltic) population had the smallest historical Ne among the collared flycatchers. Analysis of pairwise IBD in Baltic collared flycatchers indicated that this population was founded <60 generations ago. This study provides a rare genomic glimpse into demographic history and the mechanisms underlying the genome-wide distribution of ROH.
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119
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Wang RJ, Gray MM, Parmenter MD, Broman KW, Payseur BA. Recombination rate variation in mice from an isolated island. Mol Ecol 2016; 26:457-470. [PMID: 27864900 DOI: 10.1111/mec.13932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023]
Abstract
Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales.
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Affiliation(s)
- Richard J Wang
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Michelle D Parmenter
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Karl W Broman
- Department of Biostatistics & Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
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120
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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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121
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Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. Mol Ecol Resour 2016; 17:586-597. [DOI: 10.1111/1755-0998.12602] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 09/02/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ludovic Dutoit
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Reto Burri
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Alexander Nater
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
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122
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Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL. Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Mol Ecol 2016; 25:4488-507. [PMID: 27484941 DOI: 10.1111/mec.13792] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022]
Abstract
Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this 'sweep-before-differentiation' model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Miguel Alcaide
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Kira E Delmore
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Jessica H Irwin
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Gregory L Owens
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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123
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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124
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Safran RJ, Scordato ESC, Wilkins MR, Hubbard JK, Jenkins BR, Albrecht T, Flaxman SM, Karaardıç H, Vortman Y, Lotem A, Nosil P, Pap P, Shen S, Chan S, Parchman T, Kane NC. Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation. Mol Ecol 2016; 25:3865-83. [DOI: 10.1111/mec.13740] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- R. J. Safran
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - E. S. C. Scordato
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - M. R. Wilkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - J. K. Hubbard
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - B. R. Jenkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - T. Albrecht
- Department of Zoology Charles University in Prague and Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Prague Czech Republic
| | - S. M. Flaxman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - H. Karaardıç
- Elementary Science Education Department Education Faculty Alanya Alaaddin Keykubat University Alanya Turkey
| | - Y. Vortman
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
- Hula Research Center Department of Animal Sciences Tel‐Hai College Israel
| | - A. Lotem
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
| | - P. Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - P. Pap
- Department of Taxonomy and Ecology Babeş‐Bolyai University Cluj‐Napoca Romania
| | - S. Shen
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - S.‐F. Chan
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - T.L. Parchman
- Department of Biology University of Nevada Reno NV USA
| | - N. C. Kane
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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125
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Smeds L, Qvarnström A, Ellegren H. Direct estimate of the rate of germline mutation in a bird. Genome Res 2016; 26:1211-8. [PMID: 27412854 PMCID: PMC5052036 DOI: 10.1101/gr.204669.116] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/12/2016] [Indexed: 12/30/2022]
Abstract
The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10(-9), which corresponds to 2.3 × 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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126
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Smeds L, Mugal CF, Qvarnström A, Ellegren H. High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree. PLoS Genet 2016; 12:e1006044. [PMID: 27219623 PMCID: PMC4878770 DOI: 10.1371/journal.pgen.1006044] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/19/2016] [Indexed: 01/04/2023] Open
Abstract
Recombination is an engine of genetic diversity and therefore constitutes a key process in evolutionary biology and genetics. While the outcome of crossover recombination can readily be detected as shuffled alleles by following the inheritance of markers in pedigreed families, the more precise location of both crossover and non-crossover recombination events has been difficult to pinpoint. As a consequence, we lack a detailed portrait of the recombination landscape for most organisms and knowledge on how this landscape impacts on sequence evolution at a local scale. To localize recombination events with high resolution in an avian system, we performed whole-genome re-sequencing at high coverage of a complete three-generation collared flycatcher pedigree. We identified 325 crossovers at a median resolution of 1.4 kb, with 86% of the events localized to <10 kb intervals. Observed crossover rates were in excellent agreement with data from linkage mapping, were 52% higher in male (3.56 cM/Mb) than in female meiosis (2.28 cM/Mb), and increased towards chromosome ends in male but not female meiosis. Crossover events were non-randomly distributed in the genome with several distinct hot-spots and a concentration to genic regions, with the highest density in promoters and CpG islands. We further identified 267 non-crossovers, whose location was significantly associated with crossover locations. We detected a significant transmission bias (0.18) in favour of 'strong' (G, C) over 'weak' (A, T) alleles at non-crossover events, providing direct evidence for the process of GC-biased gene conversion in an avian system. The approach taken in this study should be applicable to any species and would thereby help to provide a more comprehensive portray of the recombination landscape across organism groups.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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127
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Husby A, Kawakami T, Rönnegård L, Smeds L, Ellegren H, Qvarnström A. Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait. Proc Biol Sci 2016; 282:20150156. [PMID: 25833857 PMCID: PMC4426624 DOI: 10.1098/rspb.2015.0156] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Understanding the genetic basis of traits involved in adaptation is a major
challenge in evolutionary biology but remains poorly understood. Here, we use
genome-wide association mapping using a custom 50 k single nucleotide
polymorphism (SNP) array in a natural population of collared flycatchers to
examine the genetic basis of clutch size, an important life-history trait in
many animal species. We found evidence for an association on chromosome 18 where
one SNP significant at the genome-wide level explained 3.9% of the
phenotypic variance. We also detected two suggestive quantitative trait loci
(QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were
generally weak and not significant, although there was some indication of a
sex-by-genotype interaction for lifetime reproductive success at the suggestive
QTL on chromosome 26. This implies that sexual antagonism may play a role in
maintaining genetic variation at this QTL. Our findings provide candidate
regions for a classic avian life-history trait that will be useful for future
studies examining the molecular and cellular function of, as well as
evolutionary mechanisms operating at, these loci.
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Affiliation(s)
- Arild Husby
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim 7491, Norway Department of Biosciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Lars Rönnegård
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
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128
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Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SMJ, Ellegren H. Divergence in gene expression within and between two closely related flycatcher species. Mol Ecol 2016; 25:2015-28. [PMID: 26928872 PMCID: PMC4879514 DOI: 10.1111/mec.13596] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
Relatively little is known about the character of gene expression evolution as species diverge. It is for instance unclear if gene expression generally evolves in a clock‐like manner (by stabilizing selection or neutral evolution) or if there are frequent episodes of directional selection. To gain insights into the evolutionary divergence of gene expression, we sequenced and compared the transcriptomes of multiple organs from population samples of collared (Ficedula albicollis) and pied flycatchers (F. hypoleuca), two species which diverged less than one million years ago. Ordination analysis separated samples by organ rather than by species. Organs differed in their degrees of expression variance within species and expression divergence between species. Variance was negatively correlated with expression breadth and protein interactivity, suggesting that pleiotropic constraints reduce gene expression variance within species. Variance was correlated with between‐species divergence, consistent with a pattern expected from stabilizing selection and neutral evolution. Using an expression PST approach, we identified genes differentially expressed between species and found 16 genes uniquely expressed in one of the species. For one of these, DPP7, uniquely expressed in collared flycatcher, the absence of expression in pied flycatcher could be associated with a ≈20‐kb deletion including 11 of 13 exons. This study of a young vertebrate speciation model system expands our knowledge of how gene expression evolves as natural populations become reproductively isolated.
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Affiliation(s)
- Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Axel Künstner
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Hannu Mäkinen
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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129
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Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. The Time Scale of Recombination Rate Evolution in Great Apes. Mol Biol Evol 2016; 33:928-45. [PMID: 26671457 PMCID: PMC5870646 DOI: 10.1093/molbev/msv331] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.
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Affiliation(s)
- Laurie S Stevison
- Institute for Human Genetics, University of California San Francisco Department of Biological Sciences, Auburn University
| | - August E Woerner
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Genetics, University of Arizona
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University Department of Genetics, Stanford University
| | - Krishna R Veeramah
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolution, Stony Brook University
| | - Kimberly F McManus
- Department of Biology, Stanford University Department of Biomedical Informatics, Stanford University
| | | | - Michael F Hammer
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona Department of Ecology and Evolutionary Biology, University of Arizona Department of Anthropology, University of Arizona
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco Department of Epidemiology & Biostatistics, University of California San Francisco
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130
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Kim KW, Griffith SC, Burke T. Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae). Heredity (Edinb) 2016; 116:409-16. [PMID: 26786066 PMCID: PMC4806697 DOI: 10.1038/hdy.2015.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/25/2015] [Accepted: 12/11/2015] [Indexed: 01/04/2023] Open
Abstract
Colour polymorphism is known to facilitate speciation but the genetic basis of animal pigmentation and how colour polymorphisms contribute to speciation is poorly understood. Restricted recombination may promote linkage disequilibrium between the colour locus and incompatibility genes. Genomic rearrangement and the position of relevant loci within a chromosome are important factors that influence the frequency of recombination. Therefore, it is important to know the position of the colour locus, gene order and recombination landscape of the chromosome to understand the mechanism that generates incompatibilities between morphs. Recent studies showed remarkable pre- and postzygotic incompatibilities between sympatric colour morphs of the Gouldian finch (Erythrura gouldiae), in which head feather colour is genetically determined by a single sex-linked locus, Red. We constructed a genetic map for the Z chromosome of the Gouldian finch (male-specific map distance=131 cM), using 618 captive-bred birds and 34 microsatellite markers, to investigate the extent of inter- and intraspecific genomic rearrangements and variation in recombination rate within the Z chromosome. We refined the location of the Red locus to a ~7.2-cM interval in a region with a moderate recombination rate but outside the least-recombining, putative centromeric region. There was no evidence of chromosome-wide genomic rearrangements between the chromosomes carrying the red or black alleles with the current marker resolution. This work will contribute to identifying the causal gene, which will in turn enable alternative explanations for the association between incompatibility and colouration, such as fine-scale linkage disequilibrium, genomic rearrangements and pleiotropy, to be tested.
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Affiliation(s)
- K-W Kim
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - S C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - T Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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131
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Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene. Genetics 2016; 203:525-41. [PMID: 27017626 PMCID: PMC4858797 DOI: 10.1534/genetics.115.183285] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
Abstract
A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects.
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132
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Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Mol Biol Evol 2016; 33:1517-27. [DOI: 10.1093/molbev/msw033] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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133
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Wellenreuther M, Hansson B. Detecting Polygenic Evolution: Problems, Pitfalls, and Promises. Trends Genet 2016; 32:155-164. [DOI: 10.1016/j.tig.2015.12.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
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134
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Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H. PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Mol Ecol 2016; 25:1058-72. [PMID: 26797914 PMCID: PMC4793928 DOI: 10.1111/mec.13540] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 12/15/2015] [Accepted: 01/07/2016] [Indexed: 12/12/2022]
Abstract
Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (Ne ) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in Ne over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black-and-white flycatchers. Ne curves of Atlas, collared, pied and semicollared flycatcher converged 1-2 million years ago (Ma) at an Ne of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate Ne trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100-200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in Ne differed among species, and for pied flycatcher, the temporal dynamics of Ne differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of ≥18X, a per-site filter of ≥10 reads and no more than 25% of missing data.
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Affiliation(s)
- Krystyna Nadachowska-Brzyska
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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135
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Davey JW, Chouteau M, Barker SL, Maroja L, Baxter SW, Simpson F, Merrill RM, Joron M, Mallet J, Dasmahapatra KK, Jiggins CD. Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution. G3 (BETHESDA, MD.) 2016; 6:695-708. [PMID: 26772750 PMCID: PMC4777131 DOI: 10.1534/g3.115.023655] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022]
Abstract
The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.
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Affiliation(s)
- John W Davey
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
| | - Mathieu Chouteau
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France
| | - Sarah L Barker
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
| | - Luana Maroja
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Fraser Simpson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | | | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France
| | - James Mallet
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | - Kanchon K Dasmahapatra
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
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136
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del Priore L, Pigozzi MI. Heterologous Synapsis and Crossover Suppression in Heterozygotes for a Pericentric Inversion in the Zebra Finch. Cytogenet Genome Res 2015; 147:154-60. [DOI: 10.1159/000442656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 11/19/2022] Open
Abstract
In the zebra finch, 2 alternative morphs regarding centromere position were described for chromosome 6. This polymorphism was interpreted to be the result of a pericentric inversion, but other causes of the centromere repositioning were not ruled out. We used immunofluorescence localization to examine the distribution of MLH1 foci on synaptonemal complexes to test the prediction that pericentric inversions cause synaptic irregularities and/or crossover suppression in heterozygotes. We found complete suppression of crossing over in the region involved in the rearrangement in male and female heterozygotes. In contrast, the same region showed high levels of crossing over in homozygotes for the acrocentric form of this chromosome. No inversion loops or synaptic irregularities were detected along bivalent 6 in heterozygotes suggesting that heterologous pairing is achieved during zygotene or early pachytene. Altogether these findings strongly indicate that the polymorphic chromosome 6 originated by a pericentric inversion. Since inversions are common rearrangements in karyotypic evolution in birds, it seems likely that early heterologous pairing could help to fix these rearrangements, preventing crossing overs in heterozygotes and their deleterious effects on fertility.
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137
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Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H. Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Mol Ecol Resour 2015; 16:727-41. [PMID: 26649993 DOI: 10.1111/1755-0998.12498] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/18/2015] [Accepted: 11/30/2015] [Indexed: 12/24/2022]
Abstract
Dissecting the genetic basis of phenotypic variation in natural populations is a long-standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large-effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 whole-genome-resequenced male collared flycatchers with extreme phenotypes, and on 415 males sampled independent of patch size and genotyped with a 50K SNP chip. No SNPs were genomewide statistically significantly associated with patch size. Simulation-based power analyses suggest that the power to detect large-effect loci responsible for 10% of phenotypic variance was <0.5 in the genome resequencing analysis, and <0.1 in the SNP chip analysis. Reducing the recombination by two-thirds relative to collared flycatchers modestly increased power. Tripling sample size increased power to >0.8 for resequencing of extreme phenotypes (N = 243), but power remained <0.2 for the 50K SNP chip analysis (N = 1245). At least 1 million SNPs were necessary to achieve power >0.8 when analysing 415 randomly sampled phenotypes. However, power of the 50K SNP chip to detect large-effect loci was nearly 0.8 in simulations with a small effective population size of 1500. These results suggest that reliably detecting large-effect trait loci in large natural populations will often require thousands of individuals and near complete sampling of the genome. Encouragingly, far fewer individuals and loci will often be sufficient to reliably detect large-effect loci in small populations with widespread strong linkage disequilibrium.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Arild Husby
- Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, 00014, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - S Eryn McFarlane
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
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138
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Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M. Stable recombination hotspots in birds. Science 2015; 350:928-32. [PMID: 26586757 PMCID: PMC4864528 DOI: 10.1126/science.aad0843] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.
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Affiliation(s)
- Sonal Singhal
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Ellen M Leffler
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Keerthi Sannareddy
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Isaac Turner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Oliver Venn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Daniel M Hooper
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alva I Strand
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qiye Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brian Raney
- Center for Biomolecular Science and Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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139
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Manthey JD, Robbins MB, Moyle RG. A genomic investigation of the putative contact zone between divergent Brown Creeper (Certhia americana) lineages: chromosomal patterns of genetic differentiation. Genome 2015; 59:115-25. [PMID: 26794151 DOI: 10.1139/gen-2015-0093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sky islands, or montane forest separated by different lowland habitats, are highly fragmented regions that potentially limit gene flow between isolated populations. In the sky islands of the Madrean Archipelago (Arizona, USA), various taxa display different phylogeographic patterns, from unrestricted gene flow among sky islands to complex patterns with multiple distinct lineages. Using genomic-level approaches allows the investigation of differential patterns of gene flow, selection, and genetic differentiation among chromosomes and specific genomic regions between sky island populations. Here, we used thousands of SNPs to investigate the putative contact zone of divergent Brown Creeper (Certhia americana) lineages in the Madrean Archipelago sky islands. We found the two lineages to be completely allopatric (during the breeding season) with a lack of hybridization and gene flow between lineages and no genetic structure among sky islands within lineages. Additionally, the two lineages inhabit different climatic and ecosystem conditions and have many local primary song dialects in the southern Arizona mountain ranges. We identified a positive relationship between genetic differentiation and chromosome size, but the sex chromosome (Z) was not found to be an outlier. Differential patterns of genetic differentiation per chromosome may be explained by genetic drift--possibly in conjunction with non-random mating and non-random gene flow--due to variance in recombination rates among chromosomes.
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Affiliation(s)
- Joseph D Manthey
- a Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.,b Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Mark B Robbins
- a Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Robert G Moyle
- a Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.,b Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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140
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A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 2015; 48:79-83. [PMID: 26569125 PMCID: PMC5218575 DOI: 10.1038/ng.3443] [Citation(s) in RCA: 286] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
Three strikingly different alternative male mating morphs (aggressive “Independents”, semi-cooperative “Satellites” and female mimic “Faeders”) coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird1,2,3. Major differences in body size, ornamentation, and aggressive and mating behaviour are inherited as an autosomal polymorphism4,5. We show that development into Satellites and Faeders is determined by a supergene6,7,8 consisting of divergent alternative, dominant, non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential Centromere protein N (CENP-N) gene, and pedigree analysis confirms lethality of inversion homozygotes. We describe novel behavioural, testes size, and steroid metabolic differences among morphs, and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.
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141
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Nater A, Burri R, Kawakami T, Smeds L, Ellegren H. Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data. Syst Biol 2015; 64:1000-17. [PMID: 26187295 PMCID: PMC4604831 DOI: 10.1093/sysbio/syv045] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/24/2015] [Indexed: 01/25/2023] Open
Abstract
Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.
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Affiliation(s)
- Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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142
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Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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143
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Bolívar P, Mugal CF, Nater A, Ellegren H. Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System. Mol Biol Evol 2015; 33:216-27. [PMID: 26446902 PMCID: PMC4693978 DOI: 10.1093/molbev/msv214] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill–Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C (“strong,” S) over A:T (“weak,” W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.
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Affiliation(s)
- Paulina Bolívar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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144
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Burri R, Nater A, Kawakami T, Mugal CF, Olason PI, Smeds L, Suh A, Dutoit L, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Res 2015; 25:1656-65. [PMID: 26355005 PMCID: PMC4617962 DOI: 10.1101/gr.196485.115] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/30/2015] [Indexed: 12/19/2022]
Abstract
Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of diverging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands; how the differentiation landscape evolves as speciation advances; and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence divergence (dxy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in diversity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.
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Affiliation(s)
- Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Pall I Olason
- Wallenberg Advanced Bioinformatics Infrastructure (WABI), Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway; Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway; Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
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145
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Suh A, Smeds L, Ellegren H. The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds. PLoS Biol 2015; 13:e1002224. [PMID: 26284513 PMCID: PMC4540587 DOI: 10.1371/journal.pbio.1002224] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/10/2015] [Indexed: 12/18/2022] Open
Abstract
The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree. A study of ancient genetic variation reveals genomic evidence for near-simultaneous speciation at the base of Neoaves (a group containing most modern birds), which temporally coincides with the mass extinction of nonavian dinosaurs and archaic birds. The rise of modern birds began after the mass extinction of nonavian dinosaurs and archaic birds at the Cretaceous-Paleogene (K-Pg) boundary, about 66 million years ago. This coincides with the super-rapid adaptive radiation of Neoaves (a group that contains most modern birds), which has been difficult to resolve even with whole genome sequences. We reconstructed the genealogical fates of thousands of rare genomic changes (insertions of selfish mobile elements called retrotransposons), a third of which were found to be affected by a phenomenon known as incomplete lineage sorting (ILS), namely a persistence of polymorphisms across multiple successive speciation events. Astoundingly, we found that near the K-Pg boundary, speciation events were accompanied by extreme levels of ILS, suggesting a near-simultaneous, star-like diversification process that appears plausible in the context of instantaneous niche availability that must have followed the K-Pg mass extinction. Our genome-scale results provide a population genomic explanation as to why some species radiations may be more complex than a fully bifurcating tree of life. We suggest that, under such circumstances, ILS bears witness to the biological limitation of phylogenetic resolution.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
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146
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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147
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A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing. Genetics 2015; 201:31-8. [PMID: 26116153 DOI: 10.1534/genetics.115.179028] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/24/2015] [Indexed: 12/12/2022] Open
Abstract
Genetic linkage maps are critical for assembling draft genomes to a meaningful chromosome level and for deciphering the genomic underpinnings of biological traits. The estimates of recombination rates derived from genetic maps also play an important role in understanding multiple aspects of genomic evolution such as nucleotide substitution patterns and accumulation of deleterious mutations. In this study, we developed a high-throughput experimental approach that combines fluorescence-activated cell sorting, whole-genome amplification, and short-read sequencing to construct a genetic map using single-sperm cells. Furthermore, a computational algorithm was developed to analyze single-sperm whole-genome sequencing data for map construction. These methods allowed us to rapidly build a male-specific genetic map for the freshwater microcrustacean Daphnia pulex, which shows significant improvements compared to a previous map. With a total of mapped 1672 haplotype blocks and an average intermarker distance of 0.87 cM, this map spans a total genetic distance of 1451 Kosambi cM and comprises 90% of the resolved regions in the current Daphnia reference assembly. The map also reveals the mistaken mapping of seven scaffolds in the reference assembly onto chromosome II by a previous microsatellite map based on F2 crosses. Our approach can be easily applied to many other organisms and holds great promise for unveiling the intragenomic and intraspecific variation in the recombination rates.
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148
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Fierst JL. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools. Front Genet 2015; 6:220. [PMID: 26150829 PMCID: PMC4473057 DOI: 10.3389/fgene.2015.00220] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/08/2015] [Indexed: 01/05/2023] Open
Abstract
Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.
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Affiliation(s)
- Janna L. Fierst
- Department of Biological Sciences, University of AlabamaTuscaloosa, AL, USA
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149
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Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 2015; 6:7330. [PMID: 26040272 PMCID: PMC4468903 DOI: 10.1038/ncomms8330] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/28/2015] [Indexed: 02/07/2023] Open
Abstract
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear–cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution. The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Vera Warmuth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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150
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Nietlisbach P, Camenisch G, Bucher T, Slate J, Keller LF, Postma E. A microsatellite-based linkage map for song sparrows (Melospiza melodia). Mol Ecol Resour 2015; 15:1486-96. [PMID: 25865627 DOI: 10.1111/1755-0998.12414] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 01/15/2023]
Abstract
Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.
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Affiliation(s)
- Pirmin Nietlisbach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Glauco Camenisch
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Thomas Bucher
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jon Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Lukas F Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Erik Postma
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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