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Zhao Z, Zhou Y, Wang S, Zhang X, Wang C, Li S. LDscaff: LD-based scaffolding of de novo genome assemblies. BMC Bioinformatics 2020; 21:570. [PMID: 33371875 PMCID: PMC7768660 DOI: 10.1186/s12859-020-03895-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Background Genome assembly is fundamental for de novo genome analysis. Hybrid assembly, utilizing various sequencing technologies increases both contiguity and accuracy. While such approaches require extra costly sequencing efforts, the information provided millions of existed whole-genome sequencing data have not been fully utilized to resolve the task of scaffolding. Genetic recombination patterns in population data indicate non-random association among alleles at different loci, can provide physical distance signals to guide scaffolding. Results In this paper, we propose LDscaff for draft genome assembly incorporating linkage disequilibrium information in population data. We evaluated the performance of our method with both simulated data and real data. We simulated scaffolds by splitting the pig reference genome and reassembled them. Gaps between scaffolds were introduced ranging from 0 to 100 KB. The genome misassembly rate is 2.43% when there is no gap. Then we implemented our method to refine the Giant Panda genome and the donkey genome, which are purely assembled by NGS data. After LDscaff treatment, the resulting Panda assembly has scaffold N50 of 3.6 MB, 2.5 times larger than the original N50 (1.3 MB). The re-assembled donkey assembly has an improved N50 length of 32.1 MB from 23.8 MB. Conclusions Our method effectively improves the assemblies with existed re-sequencing data, and is an potential alternative to the existing assemblers required for the collection of new data.
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Affiliation(s)
- Zicheng Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Yingxiao Zhou
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Shuai Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng City, 252059, Shandong, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China.
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Yazdi HP, Silva WTAF, Suh A. Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes. Genes (Basel) 2020; 11:E1153. [PMID: 33007827 PMCID: PMC7601716 DOI: 10.3390/genes11101153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023] Open
Abstract
The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.
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Affiliation(s)
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK;
- Department of Organismal Biology—Systematic Biology, Uppsala University, SE-752 36 Uppsala, Sweden
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53
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The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes ( Zosterops lateralis). G3-GENES GENOMES GENETICS 2020; 10:3147-3163. [PMID: 32660974 PMCID: PMC7466963 DOI: 10.1534/g3.120.401352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.
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54
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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55
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Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2020; 11:3403. [PMID: 32636372 PMCID: PMC7341801 DOI: 10.1038/s41467-020-17195-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
- Department of Biology, Pennsylvania State University, 310 Wartik Lab, University Park, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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Booker TR, Yeaman S, Whitlock MC. Variation in recombination rate affects detection of outliers in genome scans under neutrality. Mol Ecol 2020; 29:4274-4279. [DOI: 10.1111/mec.15501] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Tom R. Booker
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada
- Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Sam Yeaman
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Michael C. Whitlock
- Biodiversity Research Centre University of British Columbia Vancouver BC Canada
- Department of Zoology University of British Columbia Vancouver BC Canada
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Lutgen D, Ritter R, Olsen R, Schielzeth H, Gruselius J, Ewels P, García JT, Shirihai H, Schweizer M, Suh A, Burri R. Linked‐read sequencing enables haplotype‐resolved resequencing at population scale. Mol Ecol Resour 2020; 20:1311-1322. [DOI: 10.1111/1755-0998.13192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Dave Lutgen
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Raphael Ritter
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Remi‐André Olsen
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Holger Schielzeth
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
| | - Joel Gruselius
- Science for Life Laboratory Department of Biosciences and Nutrition Karolinska Institutet Stockholm Sweden
| | - Philip Ewels
- Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden
| | - Jesús T. García
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ciudad Real Spain
| | | | - Manuel Schweizer
- Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Alexander Suh
- Department of Organismal Biology – Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
| | - Reto Burri
- Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany
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Lundregan SL, Niskanen AK, Muff S, Holand H, Kvalnes T, Ringsby T, Husby A, Jensen H. Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge. Mol Ecol 2020; 29:3812-3829. [DOI: 10.1111/mec.15491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sarah L. Lundregan
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Stefanie Muff
- Centre for Biodiversity Dynamics Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| | - Håkon Holand
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Thor‐Harald Ringsby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Evolutionary Biology Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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Loureiro L, Engstrom M, Lim B. Optimization of Genotype by Sequencing data for phylogenetic purposes. MethodsX 2020; 7:100892. [PMID: 32373482 PMCID: PMC7195544 DOI: 10.1016/j.mex.2020.100892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/03/2020] [Indexed: 12/19/2022] Open
Abstract
• Herein we propose a framework for assembling and analyzing Genotype by Sequencing (GBS) data to better understand evolutionary relationships within a group of closely related species using the mastiff bats (Molossus) as our model system. Many species within this genus have low-levels of genetic variation within and between morphologically distinct species, and the relationships among them remain unresolved using traditional Sanger sequencing methods. Given that both de novo and reference genome pipelines can be used to assemble next generation sequences, and that several tree inference methodologies have been proposed for single nucleotide polymorphism (SNP) data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Different alignments and phylogenetic inferences produced consistent results, supporting the GBS approach for answering evolutionary questions on a macroevolutionary scale when the genetic distance among phenotypically identifiable clades is low. We highlight the importance of exploring the relationships among groups using different assembly assumptions and also distinct phylogenetic inference methods, particularly when addressing phylogenetic questions in genetic and morphologically conservative taxa. • The method uses the comparison of several filter settings, alignments, and tree inference approaches on Genotype by Sequencing data. • Consistent results were found among several approaches. • The methodology successfully recovered well supported species boundaries and phylogenetic relationships among species of mastiff bats not hypothesized by previous methods.
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Affiliation(s)
- L.O. Loureiro
- University of Toronto, Canada
- Royal Ontario Museum, Canada
| | - M.D. Engstrom
- University of Toronto, Canada
- Royal Ontario Museum, Canada
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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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Ducrest A, Neuenschwander S, Schmid‐Siegert E, Pagni M, Train C, Dylus D, Nevers Y, Warwick Vesztrocy A, San‐Jose LM, Dupasquier M, Dessimoz C, Xenarios I, Roulin A, Goudet J. New genome assembly of the barn owl ( Tyto alba alba). Ecol Evol 2020; 10:2284-2298. [PMID: 32184981 PMCID: PMC7069322 DOI: 10.1002/ece3.5991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/05/2019] [Accepted: 12/16/2019] [Indexed: 12/25/2022] Open
Abstract
New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single-Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.
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Affiliation(s)
- Anne‐Lyse Ducrest
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | | | - Marco Pagni
- Vital‐ITSwiss Institute of BioinformaticsLausanneSwitzerland
| | - Clément Train
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - David Dylus
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Yannis Nevers
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Alex Warwick Vesztrocy
- Center for Life's Origins and EvolutionDepartment of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Luis M. San‐Jose
- Laboratory Evolution and Biological DiversityUMR 5174CNRSUniversity of Toulouse III Paul SabatierToulouseFrance
| | | | - Christophe Dessimoz
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Ioannis Xenarios
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Alexandre Roulin
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Jérôme Goudet
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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Shi Y, Zhou Z, Liu B, Kong S, Chen B, Bai H, Li L, Pu F, Xu P. Construction of a High-Density Genetic Linkage Map and QTL Mapping for Growth-Related Traits in Takifugu bimaculatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:130-144. [PMID: 31900733 DOI: 10.1007/s10126-019-09938-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Takifugu bimaculatus is a euryhaline species, distributed ranging from the southern Yellow Sea to the South China Sea. Their tolerance to a wide range of salinity and temperature, coupled with a desirable firm texture, makes T. bimaculatus a strong candidate for Takifugu aquaculture in subtropics areas. Due to the increasing demand in markets and emerging of the Takifugu aquaculture industry, close attention has been paid to improvement on the T. bimaculatus production. In aquaculture, the great effort has been put into marker-assisted selective breeding, and efficient improvement was realized. However, few genetic resources on T. bimaculatus are provided so far. Aiming at understanding the genetic basis underlying important economic growth traits, facilitating genetic improvement and enriching the genetic resource in T. bimaculatus, we constructed the first genetic linkage map for T. bimaculatus via double digestion restriction-site association DNA sequencing and conducted quantitative traits locus (QTL) mapping for growth-related traits. The map comprised 1976 single nucleotide polymorphism markers distributed on 22 linkage groups (LG), with a total genetic distance of 2039.74 cM. Based on the linkage map, a chromosome-level assembly was constructed whereby we carried out comparative genomics analysis, verifying the high accuracy on contigs ordering of the linkage map. On the other hand, 18 QTLs associated with growth traits were detected on LG6, LG7, LG8, LG10, LG20, and LG21 with phenotypical variance ranging from 15.1 to 56.4%. Candidate genes participating in cartilage development, fat accumulation, and other growth-related regulation activities were identified from these QTLs, including col11a1, foxa2, and thrap3. The linkage map provided a solid foundation for chromosomes assembly and refinement. QTLs reported here unraveled the genomic architecture of some growth traits, which will advance the investigation of aquaculture breeding efforts in T. bimaculatus.
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Affiliation(s)
- Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bo Liu
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengnan Kong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Leibin Li
- Fisheries Research Institute of Fujian, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, China.
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63
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Loureiro LO, Engstrom MD, Lim BK. Single nucleotide polymorphisms (SNPs) provide unprecedented resolution of species boundaries, phylogenetic relationships, and genetic diversity in the mastiff bats (Molossus). Mol Phylogenet Evol 2020; 143:106690. [DOI: 10.1016/j.ympev.2019.106690] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/07/2019] [Accepted: 11/18/2019] [Indexed: 01/21/2023]
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Hagen IJ, Lien S, Billing AM, Elgvin TO, Trier C, Niskanen AK, Tarka M, Slate J, Sætre G, Jensen H. A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome. Mol Ecol Resour 2020; 20:544-559. [DOI: 10.1111/1755-0998.13134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 12/10/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Ingerid J. Hagen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - Anna M. Billing
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
| | - Tore O. Elgvin
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Cassandra Trier
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Alina K. Niskanen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Maja Tarka
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Department of Biology Lund University Lund Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences University of Sheffield Western Bank Sheffield UK
| | - Glenn‐Peter Sætre
- Centre for Ecological and Evolutionary Synthesis Department of Biology University of Oslo Oslo Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway
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65
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Battey CJ. Evidence of linked selection on the Z chromosome of hybridizing hummingbirds. Evolution 2020; 74:725-739. [PMID: 31859363 DOI: 10.1111/evo.13888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/01/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation ( F s t ) is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.
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Affiliation(s)
- Christopher J Battey
- Department of Biology, University of Washington, Seattle, Washington, 97403-1201.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403
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66
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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67
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White NJ, Snook RR, Eyres I. The Past and Future of Experimental Speciation. Trends Ecol Evol 2019; 35:10-21. [PMID: 31522756 DOI: 10.1016/j.tree.2019.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
Speciation is the result of evolutionary processes that generate barriers to gene flow between populations, facilitating reproductive isolation. Speciation is typically studied via theoretical models and snapshot tests in natural populations. Experimental speciation enables real-time direct tests of speciation theory and has been long touted as a critical complement to other approaches. We argue that, despite its promise to elucidate the evolution of reproductive isolation, experimental speciation has been underutilised and lags behind other contributions to speciation research. We review recent experiments and outline a framework for how experimental speciation can be implemented to address current outstanding questions that are otherwise challenging to answer. Greater uptake of this approach is necessary to rapidly advance understanding of speciation.
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Affiliation(s)
- Nathan J White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm 106-91, Sweden
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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68
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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.
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69
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Nadachowska-Brzyska K, Burri R, Ellegren H. Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers. Mol Ecol 2019; 28:2290-2304. [PMID: 30653779 PMCID: PMC6852393 DOI: 10.1111/mec.15021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/19/2023]
Abstract
Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.
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Affiliation(s)
| | - Reto Burri
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.,Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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70
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Prost S, Armstrong EE, Nylander J, Thomas GWC, Suh A, Petersen B, Dalen L, Benz BW, Blom MPK, Palkopoulou E, Ericson PGP, Irestedt M. Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. Gigascience 2019; 8:giz003. [PMID: 30689847 PMCID: PMC6497032 DOI: 10.1093/gigascience/giz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/30/2018] [Accepted: 01/10/2019] [Indexed: 12/14/2022] Open
Abstract
The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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Affiliation(s)
- Stefan Prost
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
- Department of Integrative Biology, University of California, 3040 Valley Life Science Building, Berkeley, CA 94720-3140, USA
| | - Ellie E Armstrong
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305–5020, USA
| | - Johan Nylander
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Gregg W C Thomas
- Department of Biology and School of Informatics, Computing, and Engineering, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Norbyvaegen 14-18, 75236 Uppsala, Sweden
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology,Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia
| | - Love Dalen
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Brett W Benz
- Department of Ornithology, American Museum of Natural History, Central Park West, New York, NY 10024, USA
| | - Mozes P K Blom
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Eleftheria Palkopoulou
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Per G P Ericson
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Martin Irestedt
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
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71
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Griffin DK, Larkin DM, O'Connor RE. Time lapse: A glimpse into prehistoric genomics. Eur J Med Genet 2019; 63:103640. [PMID: 30922926 PMCID: PMC7026692 DOI: 10.1016/j.ejmg.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/10/2019] [Indexed: 11/28/2022]
Abstract
For the purpose of this review, ‘time-lapse’ refers to the reconstruction of ancestral (in this case dinosaur) karyotypes using genome assemblies of extant species. Such reconstructions are only usually possible when genomes are assembled to ‘chromosome level’ i.e. a complete representation of all the sequences, correctly ordered contiguously on each of the chromosomes. Recent paleontological evidence is very clear that birds are living dinosaurs, the latest example of dinosaurs emerging from a catastrophic extinction event. Non-avian dinosaurs (ever present in the public imagination through art, and broadcast media) emerged some 240 million years ago and have displayed incredible phenotypic diversity. Here we report on our recent studies to infer the overall karyotype of the Theropod dinosaur lineage from extant avian chromosome level genome assemblies. Our work first focused on determining the likely karyotype of the avian ancestor (most likely a chicken-sized, two-legged, feathered, land dinosaur from the Jurassic period) finding karyotypic similarity to the chicken. We then took the work further to determine the likely karyotype of the bird-lizard ancestor and the chromosomal changes (chiefly translocations and inversions) that occurred between then and modern birds. A combination of bioinformatics and cross-species fluorescence in situ hybridization (zoo-FISH) uncovered a considerable number of translocations and fissions from a ‘lizard-like’ genome structure of 2n = 36–46 to one similar to that of soft-shelled turtles (2n = 66) from 275 to 255 million years ago (mya). Remarkable karyotypic similarities between some soft-shelled turtles and chicken suggests that there were few translocations from the bird-turtle ancestor (plus ∼7 fissions) through the dawn of the dinosaurs and pterosaurs, through the theropod linage and on to most to modern birds. In other words, an avian-like karyotype was in place about 240mya when the dinosaurs and pterosaurs first emerged. We mapped 49 chromosome inversions from then to the present day, uncovering some gene ontology enrichment in evolutionary breakpoint regions. This avian-like karyotype with its many (micro)chromosomes provides the basis for variation (the driver of natural selection) through increased random segregation and recombination. It may therefore contribute to the ability of dinosaurs to survive multiple extinction events, emerging each time as speciose and diverse.
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Affiliation(s)
- Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK.
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK. R.O'
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72
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Gazda MA, Andrade P, Afonso S, Dilyte J, Archer JP, Lopes RJ, Faria R, Carneiro M. Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons. Mol Biol Evol 2019; 35:1176-1189. [PMID: 29547891 DOI: 10.1093/molbev/msy030] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons. The strongest signature overlapped the CASK gene, a gene implicated in the formation of neuromuscular junctions. However, no diagnostic alleles were found between racing pigeons and other breeds, and only a small proportion of highly differentiated variants were exclusively detected in racing pigeons. We can thus conclude that very few individual genetic changes, if any, are either strictly necessary or sufficient for superior athletics and navigation. Gene expression analysis between racing and nonracing breeds revealed modest differences in muscle (213) and brain (29). These transcripts, however, showed only slightly elevated levels of genetic differentiation between the two groups, suggesting that most differential expression is not causative but likely a consequence of alterations in regulatory networks. Our results show that the unique suite of traits that enable fast flight, long endurance, and accurate navigation in racing pigeons, do not result from few loci acting as master switches but likely from a polygenic architecture that leveraged standing genetic variation available at the onset of the breed formation.
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Affiliation(s)
- Malgorzata A Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Jolita Dilyte
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - John P Archer
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ricardo J Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Rui Faria
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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73
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How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers. Genetics 2019; 212:277-285. [PMID: 30872320 PMCID: PMC6499528 DOI: 10.1534/genetics.119.301991] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population sizes that manifest as dips in diversity, and "islands" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps, and a long-standing quest in population genetics has been to unveil the relative importance of these processes. Here, we analyzed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher (Ficedula albicollis) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (including both protein-coding genes and conserved noncoding elements), we found that background selection can explain most of the observed baseline variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Therefore, our study demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.
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74
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Bolívar P, Guéguen L, Duret L, Ellegren H, Mugal CF. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biol 2019; 20:5. [PMID: 30616647 PMCID: PMC6322265 DOI: 10.1186/s13059-018-1613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations. RESULTS We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location. CONCLUSIONS Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
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Affiliation(s)
- Paulina Bolívar
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Duret
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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75
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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76
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De-Kayne R, Feulner PGD. A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication. G3 (BETHESDA, MD.) 2018; 8:3745-3755. [PMID: 30297382 PMCID: PMC6288842 DOI: 10.1534/g3.118.200552] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Abstract
Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g., chromosome number and type or sex-related structural differences, to fine scale patterns e.g., recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. "Albock", a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. "Albock" and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of loci of interest, e.g., FST outliers, along the whitefish genome as well as assisting with the de novo assembly of a whitefish reference genome.
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Affiliation(s)
- Rishi De-Kayne
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
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77
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Edme A, Zobač P, Korsten P, Albrecht T, Schmoll T, Krist M. Moderate heritability and low evolvability of sperm morphology in a species with high risk of sperm competition, the collared flycatcher Ficedula albicollis. J Evol Biol 2018; 32:205-217. [PMID: 30449037 DOI: 10.1111/jeb.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/02/2018] [Accepted: 11/14/2018] [Indexed: 12/19/2022]
Abstract
Spermatozoa represent the morphologically most diverse type of animal cells and show remarkable variation in size across and also within species. To understand the evolution of this diversity, it is important to reveal to what degree this variation is genetic or environmental in origin and whether this depends on species' life histories. Here we applied quantitative genetic methods to a pedigreed multigenerational data set of the collared flycatcher Ficedula albicollis, a passerine bird with high levels of extra-pair paternity, to partition genetic and environmental sources of phenotypic variation in sperm dimensions for the first time in a natural population. Narrow-sense heritability (h2 ) of total sperm length amounted to 0.44 ± 0.14 SE, whereas the corresponding figure for evolvability (estimated as coefficient of additive genetic variation, CVa ) was 0.02 ± 0.003 SE. We also found an increase in total sperm length within individual males between the arrival and nestling period. This seasonal variation may reflect constraints in the production of fully elongated spermatozoa shortly after arrival at the breeding grounds. There was no evidence of an effect of male age on sperm dimensions. In many previous studies on laboratory populations of several insect, mammal and avian species, heritabilities of sperm morphology were higher, whereas evolvabilities were similar. Explanations for the differences in heritability may include variation in the environment (laboratory vs. wild), intensity of sexual selection via sperm competition (high vs. low) and genetic architecture that involves unusual linkage disequilibrium coupled with overdominance in one of the studied species.
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Affiliation(s)
- Anaïs Edme
- Faculty of Science, Department of Zoology and Laboratory of Ornithology, Palacky University, Olomouc, Czech Republic
| | - Petr Zobač
- Faculty of Science, Department of Zoology and Laboratory of Ornithology, Palacky University, Olomouc, Czech Republic
| | - Peter Korsten
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Tomáš Albrecht
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Faculty of Science, Department of Zoology, Charles University in Prague, Prague, Czech Republic
| | - Tim Schmoll
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Miloš Krist
- Faculty of Science, Department of Zoology and Laboratory of Ornithology, Palacky University, Olomouc, Czech Republic.,Museum of Natural History, Olomouc, Czech Republic
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78
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Wang Q, Lu W, Yang J, Jiang L, Zhang Q, Kan X, Yang X. Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:27-36. [DOI: 10.1016/j.cbd.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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79
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Gossmann TI, Bockwoldt M, Diringer L, Schwarz F, Schumann VF. Evidence for Strong Fixation Bias at 4-fold Degenerate Sites Across Genes in the Great Tit Genome. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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80
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Corcoran P, Gossmann TI, Barton HJ, Slate J, Zeng K. Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species. Genome Biol Evol 2018; 9:2987-3007. [PMID: 29045655 PMCID: PMC5714183 DOI: 10.1093/gbe/evx213] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 02/06/2023] Open
Abstract
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.
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Affiliation(s)
- Pádraic Corcoran
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | | | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, South Yorkshire, United Kingdom
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81
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Furman BLS, Evans BJ. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems. Genome Biol Evol 2018; 10:742-755. [PMID: 29608717 PMCID: PMC5841384 DOI: 10.1093/gbe/evy045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/02/2023] Open
Abstract
There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.
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Affiliation(s)
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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82
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Semenov GA, Basheva EA, Borodin PM, Torgasheva AA. High rate of meiotic recombination and its implications for intricate speciation patterns in the white wagtail (Motacilla alba). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
| | - Ekaterina A Basheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
| | - Anna A Torgasheva
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
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83
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Dutoit L, Mugal CF, Bolívar P, Wang M, Nadachowska-Brzyska K, Smeds L, Yazdi HP, Gustafsson L, Ellegren H. Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome. Mol Ecol 2018; 27:3572-3581. [DOI: 10.1111/mec.14789] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/28/2018] [Accepted: 04/02/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Ludovic Dutoit
- 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
| | - Paulina Bolívar
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Mi Wang
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | | | - Linnéa Smeds
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Homa P. Yazdi
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Lars Gustafsson
- 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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84
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Lundregan SL, Hagen IJ, Gohli J, Niskanen AK, Kemppainen P, Ringsby TH, Kvalnes T, Pärn H, Rønning B, Holand H, Ranke PS, Båtnes AS, Selvik LK, Lien S, Saether BE, Husby A, Jensen H. Inferences of genetic architecture of bill morphology in house sparrow using a high-density SNP array point to a polygenic basis. Mol Ecol 2018; 27:3498-3514. [DOI: 10.1111/mec.14811] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Sarah L. Lundregan
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Ingerid J. Hagen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Norwegian Institute for Nature Research; Trondheim Norway
| | - Jostein Gohli
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Alina K. Niskanen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Department of Ecology and Genetics; University of Oulu; Oulu Finland
| | - Petri Kemppainen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
| | - Thor Harald Ringsby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Thomas Kvalnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Henrik Pärn
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Bernt Rønning
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Håkon Holand
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Peter S. Ranke
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Anna S. Båtnes
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Linn-Karina Selvik
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics; Department of Animal and Aquacultural Sciences; Faculty of Life Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Bernt-Erik Saether
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
| | - Arild Husby
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
- Organismal and Evolutionary Biology Research Programme; University of Helsinki; Helsinki Finland
- Department of Ecology and Genetics; EBC; Uppsala University; Uppsala Sweden
| | - Henrik Jensen
- Department of Biology; Centre for Biodiversity Dynamics; Norwegian University of Science and Technology; Trondheim Norway
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85
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Yazdi HP, Ellegren H. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biol Evol 2018; 10:2049-2060. [PMID: 30099482 PMCID: PMC6105114 DOI: 10.1093/gbe/evy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (≈60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.
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Affiliation(s)
- Homa Papoli Yazdi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
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86
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Sigeman H, Ponnikas S, Videvall E, Zhang H, Chauhan P, Naurin S, Hansson B. Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat. Genes (Basel) 2018; 9:genes9080373. [PMID: 30049999 PMCID: PMC6116046 DOI: 10.3390/genes9080373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023] Open
Abstract
Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Suvi Ponnikas
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Elin Videvall
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Hongkai Zhang
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Sara Naurin
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
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87
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Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nat Ecol Evol 2018; 2:1258-1267. [DOI: 10.1038/s41559-018-0606-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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88
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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89
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Haenel Q, Laurentino TG, Roesti M, Berner D. Meta-analysis of chromosome-scale crossover rate variation in eukaryotes and its significance to evolutionary genomics. Mol Ecol 2018; 27:2477-2497. [PMID: 29676042 DOI: 10.1111/mec.14699] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant and fungal species. Our quantitative analysis reveals a strong and taxonomically widespread reduction of the crossover rate in the centre of chromosomes relative to their peripheries. We demonstrate that this pattern is poorly explained by the position of the centromere, but find that the magnitude of the relative reduction in the crossover rate in chromosome centres increases with chromosome length. That is, long chromosomes often display a dramatically low crossover rate in their centre, whereas short chromosomes exhibit a relatively homogeneous crossover rate. This observation is compatible with a model in which crossover is initiated from the chromosome tips, an idea with preliminary support from mechanistic investigations of meiotic recombination. Consequently, we show that organisms achieve a higher genome-wide crossover rate by evolving smaller chromosomes. Summarizing theory and providing empirical examples, we finally highlight that taxonomically widespread and systematic heterogeneity in crossover rate along chromosomes generates predictable broad-scale trends in genetic diversity and population differentiation by modifying the impact of natural selection among regions within a genome. We conclude by emphasizing that chromosome-scale heterogeneity in crossover rate should urgently be incorporated into analytical tools in evolutionary genomics, and in the interpretation of resulting patterns.
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Affiliation(s)
- Quiterie Haenel
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
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90
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O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun 2018; 9:1883. [PMID: 29784931 PMCID: PMC5962605 DOI: 10.1038/s41467-018-04267-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 01/07/2023] Open
Abstract
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning. Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.
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Affiliation(s)
- Rebecca E O'Connor
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael N Romanov
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Lucas G Kiazim
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, IA, 50011, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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91
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Tiley GP, Kimball RT, Braun EL, Burleigh JG. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 2018; 19:336. [PMID: 29739321 PMCID: PMC5941490 DOI: 10.1186/s12864-018-4711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care. We sequenced the genome of Bambusicola thoracicus (Chinese Bamboo Partridge) using a single insert library to test hypotheses about genome evolution in galliforms. Selection acting at the phenotypic level could result in more evidence of positive selection in the Gallus genome than in Bambusicola. However, the historical range size of Bambusicola was likely smaller than Gallus, and demographic effects could lead to higher rates of nonsynonymous substitution in Bambusicola than in Gallus. RESULTS We generated a genome assembly suitable for evolutionary analyses. We examined the impact of selection on coding regions by examining shifts in the average nonsynonymous to synonymous rate ratio (dN/dS) and the proportion of sites subject to episodic positive selection. We observed elevated dN/dS in Bambusicola relative to Gallus, which is consistent with our hypothesis that demographic effects may be important drivers of genome evolution in Bambusicola. We also demonstrated that alignment error can greatly inflate estimates of the number of genes that experienced episodic positive selection and heterogeneity in dN/dS. However, overall patterns of molecular evolution were robust to alignment uncertainty. Bambusicola thoracicus has higher estimates of heterozygosity than Gallus gallus, possibly due to migration events over the past 100,000 years. CONCLUSIONS Our results emphasized the importance of demographic processes in generating the patterns of variation between Bambusicola and Gallus. We also demonstrated that genome assemblies generated using a single library can provide valuable insights into avian evolutionary history and found that it is important to account for alignment uncertainty in evolutionary inferences from draft genomes.
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Affiliation(s)
- G P Tiley
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA. .,Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - R T Kimball
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - E L Braun
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - J G Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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92
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Sefick SA, Castronova MA, Stevison LS. genotypeR
: An integrated
r
package for single nucleotide polymorphism genotype marker design and data analysis. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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93
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Gui S, Peng J, Wang X, Wu Z, Cao R, Salse J, Zhang H, Zhu Z, Xia Q, Quan Z, Shu L, Ke W, Ding Y. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:721-734. [PMID: 29575237 DOI: 10.1111/tpj.13894] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 05/11/2023]
Abstract
Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
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Affiliation(s)
- Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihua Wu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Cao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jérôme Salse
- Paleogenomics & Evolution (PaleoEvo) Group, Génétique Diversité & Ecophysiologie des Céréales (GDEC), Institut National de la Recherché Agronomique UMR 1095, Clermont-Ferrand, 63100, France
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiuju Xia
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Zhiwu Quan
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Liping Shu
- Wuhan Ice-Harbor Biological Technology Co. Ltd, Wuhan, 430040, China
| | - Wedong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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94
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Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski JR, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O'Connell BL, Peck M, Pipes ML, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE, Shapiro B. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 2018; 358:951-954. [PMID: 29146814 DOI: 10.1126/science.aao0960] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/28/2017] [Indexed: 12/13/2022]
Abstract
The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction.
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Affiliation(s)
- Gemma G R Murray
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | - André E R Soares
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | - Ben J Novak
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Revive & Restore, Sausalito, CA 94965, USA
| | - Nathan K Schaefer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | - Andrew Doll
- Department of Zoology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | - Rute R Da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tara L Fulton
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Environment and Climate Change Canada, 9250-49th Street, Edmonton, AB T6B 1K5, Canada
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,NTNU University Museum, 7491 Trondheim, Norway
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Tromsø University Museum, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Brandon Letts
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - George McIntosh
- Collections Department, Rochester Museum and Science Center, Rochester, NY 14607, USA
| | - Brendan L O'Connell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Peck
- Department of Zoology, Denver Museum of Nature and Science, Denver, CO 80205, USA
| | | | - Edward S Rice
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kathryn M Santos
- Collections Department, Rochester Museum and Science Center, Rochester, NY 14607, USA
| | | | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,University of California Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,University of California Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA. .,University of California Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
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95
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Delmore KE, Lugo Ramos JS, Van Doren BM, Lundberg M, Bensch S, Irwin DE, Liedvogel M. Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds. Evol Lett 2018; 2:76-87. [PMID: 30283666 PMCID: PMC6121856 DOI: 10.1002/evl3.46] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST ) and absolute (dXY ) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window-based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY ), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.
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Affiliation(s)
- Kira E Delmore
- Max Planck Institute for Evolutionary Biology Behavioural Genomics 24306 Plön Germany
| | - Juan S Lugo Ramos
- Max Planck Institute for Evolutionary Biology Behavioural Genomics 24306 Plön Germany
| | - Benjamin M Van Doren
- Edward Grey Institute, Department of Zoology University of Oxford OX1 3PS Oxford United Kingdom
| | - Max Lundberg
- Lund University Department of Biology 223 62 Lund Sweden
| | - Staffan Bensch
- Lund University Department of Biology 223 62 Lund Sweden
| | - Darren E Irwin
- Biodiversity Research Center University of British Columbia V6T 1Z4 Vancouver British Columbia Canada
| | - Miriam Liedvogel
- Max Planck Institute for Evolutionary Biology Behavioural Genomics 24306 Plön Germany
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96
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Dapper AL, Payseur BA. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium. Mol Biol Evol 2018; 35:335-353. [PMID: 29045724 PMCID: PMC5850621 DOI: 10.1093/molbev/msx272] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots.
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Affiliation(s)
- Amy L Dapper
- Laboratory of Genetics, University of Wisconsin, Madison, WI
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
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97
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Nietlisbach P, Keller LF, Camenisch G, Guillaume F, Arcese P, Reid JM, Postma E. Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. Proc Biol Sci 2018; 284:rspb.2016.2763. [PMID: 28250184 DOI: 10.1098/rspb.2016.2763] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 01/14/2023] Open
Abstract
Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Erik Postma
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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98
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Craig RJ, Suh A, Wang M, Ellegren H. Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis). Mol Ecol 2018; 27:476-492. [DOI: 10.1111/mec.14462] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rory J. Craig
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; Edinburgh UK
| | - Alexander Suh
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Mi Wang
- 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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99
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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100
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