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Liu Y, Chen L, Duan XZ, Zhao DS, Sun JT, Hong XY. Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:2362-2368. [PMID: 31145796 DOI: 10.1093/jee/toz145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 06/09/2023]
Abstract
Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.
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Affiliation(s)
- Yan Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xing-Zhi Duan
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Dian-Shu Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Sun JT, Duan XZ, Hoffmann AA, Liu Y, Garvin MR, Chen L, Hu G, Zhou JC, Huang HJ, Xue XF, Hong XY. Mitochondrial variation in small brown planthoppers linked to multiple traits and probably reflecting a complex evolutionary trajectory. Mol Ecol 2019; 28:3306-3323. [PMID: 31183910 DOI: 10.1111/mec.15148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022]
Abstract
While it has been proposed in several taxa that the mitochondrial genome is associated with adaptive evolution to different climatic conditions, making links between mitochondrial haplotypes and organismal phenotypes remains a challenge. Mitonuclear discordance occurs in the small brown planthopper (SBPH), Laodelphax striatellus, with one mitochondrial haplogroup (HGI) more common in the cold climate region of China relative to another form (HGII) despite strong nuclear gene flow, providing a promising model to investigate climatic adaptation of mitochondrial genomes. We hypothesized that cold adaptation through HGI may be involved, and considered mitogenome evolution, population genetic analyses, and bioassays to test this hypothesis. In contrast to our hypothesis, chill-coma recovery tests and population genetic tests of selection both pointed to HGII being involved in cold adaptation. Phylogenetic analyses revealed that HGII is nested within HGI, and has three nonsynonymous changes in ND2, ND5 and CYTB in comparison to HGI. These molecular changes likely increased mtDNA copy number, cold tolerance and fecundity of SBPH, particularly through a function-altering amino acid change involving M114T in ND2. Nuclear background also influenced fecundity and chill recovery (i.e., mitonuclear epistasis) and protein modelling indicates possible nuclear interactions for the two nonsynonymous changes in ND2 and CYTB. The high occurrence frequency of HGI in the cold climate region of China remains unexplained, but several possible reasons are discussed. Overall, our study points to a link between mtDNA variation and organismal-level evolution and suggests a possible role of mitonuclear interactions in maintaining mtDNA diversity.
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Affiliation(s)
- Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xing-Zhi Duan
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yan Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Michael R Garvin
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Gao Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jin-Cheng Zhou
- Department of Entomology, Shengyang Agricultural University, Shenyang, China
| | - Hai-Jian Huang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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4
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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6
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Krzemińska U, Morales HE, Greening C, Nyári ÁS, Wilson R, Song BK, Austin CM, Sunnucks P, Pavlova A, Rahman S. Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens). Heredity (Edinb) 2017; 120:296-309. [PMID: 29180719 DOI: 10.1038/s41437-017-0020-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 11/09/2022] Open
Abstract
The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
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Affiliation(s)
- Urszula Krzemińska
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia. .,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia. .,Department of Genetics and Animal Breeding, Faculty of Animal Sciences, Warsaw University of Life Sciences SGGW, Warsaw, Poland.
| | - Hernán E Morales
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia.,Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE 405 30, Sweden
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Árpád S Nyári
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA
| | - Robyn Wilson
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Christopher M Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
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7
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Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
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Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
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