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Perez de Souza L, Bitocchi E, Papa R, Tohge T, Fernie AR. Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1021-1036. [PMID: 37272491 DOI: 10.1111/tpj.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023]
Abstract
The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Takayuki Tohge
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, Potsdam-Golm, 14476, Germany
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Tóth EG, Cseke K, Benke A, Lados BB, Tomov VT, Zhelev P, Kámpel JD, Borovics A, Köbölkuti ZA. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (Edinb) 2023:10.1038/s41437-023-00629-2. [PMID: 37316726 PMCID: PMC10382515 DOI: 10.1038/s41437-023-00629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.
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Affiliation(s)
- Endre Gy Tóth
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Botond B Lados
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Vladimir T Tomov
- Department of Landscape Architecture, Faculty of Ecology and Landscape Architecture, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, Faculty of Forestry, University of Forestry (UF), Kliment Ohridsky 10, Sofia, 1797, Bulgaria
| | - József D Kámpel
- Ottó Herman Environmental and Agricultural Technical School, Vocational School and College (Agricultural Vocational Centre of the Kisalföld Region), Ernuszt Kelemen 1, Szombathely, 9700, Hungary
| | - Attila Borovics
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
| | - Zoltán A Köbölkuti
- Department of Forest Tree Breeding, Forest Research Institute (UOS-FRI), University of Sopron, Várkerület 30/A, Sárvár, 9600, Hungary
- Departement of Applied Forest Genetics Research, Bavarian Office for Forest Genetics (AWG), Forstamtsplatz 1, Teisendorf, 83317, Germany
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Kurland S, Rafati N, Ryman N, Laikre L. Genomic dynamics of brown trout populations released to a novel environment. Ecol Evol 2022; 12:e9050. [PMID: 35813906 PMCID: PMC9251865 DOI: 10.1002/ece3.9050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/04/2022] [Accepted: 06/04/2022] [Indexed: 11/15/2022] Open
Abstract
Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.
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Affiliation(s)
- Sara Kurland
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Nima Rafati
- Department of Medical Biochemistry and MicrobiologyNational Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Nils Ryman
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Linda Laikre
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
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Cao Z, Cui L, Liu Q, Liu F, Zhao Y, Guo K, Hu T, Zhang F, Sheng X, Wang X, Peng Z, Dai M. Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China. Microbiol Spectr 2022; 10:e0251821. [PMID: 35467399 PMCID: PMC9241693 DOI: 10.1128/spectrum.02518-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/27/2022] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.
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Affiliation(s)
- Zhengzheng Cao
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Luqing Cui
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Quan Liu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Fangjia Liu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Yue Zhao
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Kaixuan Guo
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Tianyu Hu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Fan Zhang
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Xijing Sheng
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Xiangru Wang
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Zhong Peng
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
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Liu X, Li C, Cao J, Zhang X, Wang C, He J, Xing G, Wang W, Zhao J, Gai J. Growth period QTL-allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1624-1643. [PMID: 34618996 DOI: 10.1111/tpj.15531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Soybean (Glycine max (L.) Merr.) has been disseminated globally as a photoperiod/temperature-sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL-allele constitution using restricted two-stage multi-locus genome-wide association study (RTM-GWAS). Genotypes with 20 701 genome-wide SNPLDBs (single-nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL-allele matrix characterized with all QTL-allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10-12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12-21 days) or slower maturation (14-56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi-functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL-alleles relatively thoroughly using RTM-GWAS for direct matrix comparisons and subsequent analysis.
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Affiliation(s)
- Xueqin Liu
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, China
| | - Chunyan Li
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Jiqiu Cao
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Xiaoyan Zhang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Shengfeng Experiment station, Shengfeng Seed Company Limited, Jining, 272100, China
| | - Can Wang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianbo He
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangnan Xing
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wubin Wang
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinming Zhao
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junyi Gai
- Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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6
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Sinclair-Waters M, Piavchenko N, Ruokolainen A, Aykanat T, Erkinaro J, Primmer CR. Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus. Mol Ecol 2021; 31:562-570. [PMID: 34716945 DOI: 10.1111/mec.16256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022]
Abstract
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Nikolai Piavchenko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
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González‐Serna MJ, Cordero PJ, Ortego J. Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust ( Dociostaurus maroccanus). Ecol Evol 2020; 10:3991-4008. [PMID: 32489626 PMCID: PMC7244894 DOI: 10.1002/ece3.6165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.
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Affiliation(s)
- María José González‐Serna
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
- Departamento de Ciencia y Tecnología Agroforestal y GenéticaEscuela Técnica Superior de Ingenieros Agrónomos (ETSIA)Universidad de Castilla‐La Mancha (UCLM)Ciudad RealSpain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana – EBD – (CSIC)SevilleSpain
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Cullingham CI, Peery RM, Fortier CE, Mahon EL, Cooke JEK, Coltman DW. Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system. Evol Appl 2020; 13:48-61. [PMID: 31892943 PMCID: PMC6935584 DOI: 10.1111/eva.12773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack-associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.
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Affiliation(s)
| | - Rhiannon M. Peery
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Colleen E. Fortier
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Elizabeth L. Mahon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Department of Wood ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Janice E. K. Cooke
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - David W. Coltman
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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9
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Kastally C, Trasoletti M, Mardulyn P. Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps. J Evol Biol 2019; 32:1406-1417. [DOI: 10.1111/jeb.13538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Chedly Kastally
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Marta Trasoletti
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
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10
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Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout. G3-GENES GENOMES GENETICS 2019; 9:2887-2896. [PMID: 31289024 PMCID: PMC6723140 DOI: 10.1534/g3.119.400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
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11
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Loria A, Cristescu ME, Gonzalez A. Mixed evidence for adaptation to environmental pollution. Evol Appl 2019; 12:1259-1273. [PMID: 31417613 PMCID: PMC6691217 DOI: 10.1111/eva.12782] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/12/2019] [Indexed: 12/25/2022] Open
Abstract
Adaptation to pollution has been studied since the first observations of heavy metal tolerance in plants decades ago. To document micro-evolutionary responses to pollution, researchers have used phenotypic, molecular genetics, and demographic approaches. We reviewed 258 articles and evaluated the evidence for adaptive responses following exposure to a wide range of pollutants, across multiple taxonomic groups. We also conducted a meta-analysis to calculate the magnitude of phenotypic change in invertebrates in response to metal pollution. The majority of studies that reported differences in responses to pollution were focused on phenotypic responses at the individual level. Most of the studies that used demographic assays in their investigations found that negative effects induced by pollution often worsened over multiple generations. Our meta-analysis did not reveal a significant relationship between metal pollution intensity and changes in the traits studied, and this was probably due to differences in coping responses among different species, the broad array of abiotic and biotic factors, and the weak statistical power of the analysis. We found it difficult to make broad statements about how likely or how common adaptation is in the presence of environmental contamination. Ecological and evolutionary responses to contamination are complex, and difficult to interpret in the context of taxonomic, and methodological biases, and the inconsistent set of approaches that have been used to study adaptation to pollution in the laboratory and in the field. This review emphasizes the need for: (a) long-term monitoring programs on exposed populations that link demography to phenotypic, genetic, and selection assays; (b) the use of standardized protocols across studies especially for similar taxa. Approaches that combine field and laboratory studies offer the greatest opportunity to reveal the complex eco-evolutionary feedback that can occur under selection imposed by pollution.
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12
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Turkmen AS, Yuan Y, Billor N. Evaluation of methods for adjusting population stratification in genome‐wide association studies: Standard versus categorical principal component analysis. Ann Hum Genet 2019; 83:454-464. [DOI: 10.1111/ahg.12339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Affiliation(s)
| | - Yuan Yuan
- Department of Mathematics & Statistics Auburn University Auburn Alabama
| | - Nedret Billor
- Department of Mathematics & Statistics Auburn University Auburn Alabama
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13
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Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, Rödin‐Mörch P, Quintela M, Richter‐Boix A, Höglund J, Laurila A. Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor
C/EBP‐1. Mol Ecol 2019; 28:2786-2801. [DOI: 10.1111/mec.15123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 Villeurbanne France
| | - Fríða Jóhannesdóttir
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - María Quintela
- Department of Population Genetics Institute of Marine Research Bergen Norway
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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14
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Mota MR, Pinheiro F, Leal BSS, Wendt T, Palma-Silva C. The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:122-132. [PMID: 30195257 DOI: 10.1111/plb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/06/2018] [Indexed: 05/02/2023]
Abstract
Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.
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Affiliation(s)
- M R Mota
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - F Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - B S S Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - T Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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15
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Martins K, Gugger PF, Llanderal‐Mendoza J, González‐Rodríguez A, Fitz‐Gibbon ST, Zhao J, Rodríguez‐Correa H, Oyama K, Sork VL. Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa. Evol Appl 2018; 11:1842-1858. [PMID: 30459833 PMCID: PMC6231481 DOI: 10.1111/eva.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 12/30/2022] Open
Abstract
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non-native habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high-elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans-Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 F ST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.
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Affiliation(s)
- Karina Martins
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Departamento de BiologiaUniversidade Federal de São CarlosSorocabaSPBrazil
| | - Paul F. Gugger
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMaryland
| | - Jesus Llanderal‐Mendoza
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Antonio González‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Sorel T. Fitz‐Gibbon
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
| | - Jian‐Li Zhao
- Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnanChina
| | - Hernando Rodríguez‐Correa
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMichoacánMéxico
| | - Victoria L. Sork
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Institute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCalifornia
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16
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Werhahn G, Senn H, Ghazali M, Karmacharya D, Sherchan AM, Joshi J, Kusi N, López-Bao JV, Rosen T, Kachel S, Sillero-Zubiri C, Macdonald DW. The unique genetic adaptation of the Himalayan wolf to high-altitudes and consequences for conservation. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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17
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Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124. [PMID: 30345391 PMCID: PMC6192448 DOI: 10.12688/wellcomeopenres.14826.1] [Citation(s) in RCA: 1574] [Impact Index Per Article: 262.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
The
PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera. Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes. Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications. The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation. Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes. There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question. In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.
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Affiliation(s)
- Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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18
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Henriques D, Wallberg A, Chávez-Galarza J, Johnston JS, Webster MT, Pinto MA. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Sci Rep 2018; 8:11145. [PMID: 30042407 PMCID: PMC6057950 DOI: 10.1038/s41598-018-29469-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.
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Affiliation(s)
- Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, La Molina, Lima, Peru
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE -751 23, Uppsala, Sweden
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal.
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19
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Coetzer WG, Turner TR, Schmitt CA, Grobler JP. Adaptive genetic variation at three loci in South African vervet monkeys ( Chlorocebus pygerythrus) and the role of selection within primates. PeerJ 2018; 6:e4953. [PMID: 29888138 PMCID: PMC5991302 DOI: 10.7717/peerj.4953] [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: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11-21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species.
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Affiliation(s)
- Willem G Coetzer
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Trudy R Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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20
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Oberprieler C, Zimmer C, Bog M. Are there morphological and life-history traits under climate-dependent differential selection in S Tunesian Diplotaxis harra (Forssk.) Boiss. (Brassicaceae) populations? Ecol Evol 2018; 8:1047-1062. [PMID: 29375778 PMCID: PMC5773308 DOI: 10.1002/ece3.3705] [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: 09/08/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
Adaptation of morphological, physiological, or life-history traits of a plant species to heterogeneous habitats through the process of natural selection is a paramount process in evolutionary biology. We have used a population genomic approach to disentangle selection-based and demography-based variation in morphological and life-history traits in the crucifer Diplotaxis harra (Forssk.) Boiss. (Brassicaceae) encountered in populations along aridity gradients in S Tunisia. We have genotyped 182 individuals from 12 populations of the species ranging from coastal to semidesert habitats using amplified fragment length polymorphism (AFLP) fingerprinting and assessed a range of morphological and life-history traits from their progeny cultivated under common-garden conditions. Application of three different statistical approaches for searching AFLP loci under selection allowed us to characterize candidate loci, for which their association with the traits assessed was tested for statistical significance and correlation with climate data. As a key result of this study, we find that only the shape of cauline leaves seems to be under differential selection along the aridity gradient in S Tunisian populations of Diplotaxis harra, while for all other traits studied neutral biogeographical and/or random factors could not be excluded as explanation for the variation observed. The counter-intuitive finding that plants from populations with more arid habitats produce broader leaves under optimal conditions of cultivation than those from more mesic habitats is interpreted as being ascribable to selection for a higher plasticity in this trait under more unpredictable semidesert conditions compared to the more predictable ones in coastal habitats.
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Affiliation(s)
- Christoph Oberprieler
- Evolutionary and Systematic Botany GroupInstitute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany GroupInstitute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Manuela Bog
- Evolutionary and Systematic Botany GroupInstitute of Plant SciencesUniversity of RegensburgRegensburgGermany
- Present address:
General Botany and Plant SystematicsInstitute of Botany and Landscape EcologyErnst Moritz Arndt University GreifswaldGreifswaldGermany
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21
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Khrustaleva AM, Klovach NV, Seeb JE. Genetic variability and population structure of sockeye salmon from the Asian Coast of Pacific Ocean. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Gilroy DL, Phillips KP, Richardson DS, van Oosterhout C. Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'. J Evol Biol 2017; 30:1276-1287. [PMID: 28370771 DOI: 10.1111/jeb.13077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/21/2017] [Indexed: 01/09/2023]
Abstract
Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations.
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Affiliation(s)
- D L Gilroy
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - K P Phillips
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - D S Richardson
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Nature Seychelles, Mahe, Republic of Seychelles
| | - C van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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23
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Wang J, Fernández‐Pavía SP, Larsen MM, Garay‐Serrano E, Gregorio‐Cipriano R, Rodríguez‐Alvarado G, Grünwald NJ, Goss EM. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin. Mol Ecol 2017; 26:1091-1107. [DOI: 10.1111/mec.14000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/11/2016] [Accepted: 12/21/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Jianan Wang
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
| | - Sylvia P. Fernández‐Pavía
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Edith Garay‐Serrano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Rosario Gregorio‐Cipriano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Gerardo Rodríguez‐Alvarado
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Erica M. Goss
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
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24
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Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG. A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits. Evol Appl 2016; 10:276-296. [PMID: 28250812 PMCID: PMC5322405 DOI: 10.1111/eva.12450] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
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Affiliation(s)
- Lei Liu
- Department of Integrative Biology University of Guelph Guelph ON Canada; Present address: School of Marine Sciences Ningbo University Ningbo China
| | | | | | - Matthew Peter Kent
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Danielle MacDonald
- Saint Andrews Biological Station Department of Fisheries and Oceans Canada Saint Andrews NB Canada
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25
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Diz AP, Calvete JJ. Ecological proteomics: is the field ripe for integrating proteomics into evolutionary ecology research? J Proteomics 2016; 135:1-3. [PMID: 26897082 DOI: 10.1016/j.jprot.2016.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, CSIC, Valencia, (Spain).
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26
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Huang W, Zhao X, Zhao X, Li Y, Lian J. Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China. Ecol Evol 2016; 6:8256-8266. [PMID: 27878093 PMCID: PMC5108275 DOI: 10.1002/ece3.2549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 09/08/2016] [Accepted: 09/22/2016] [Indexed: 12/19/2022] Open
Abstract
Caragana microphylla (Leguminosae) is a dominant climax semishrub species in northern China. We evaluated genetic variation within and among populations sampled from three different environmental gradients in Horqin Sandy Land in northern China using intersimple sequence repeats markers and investigated the possible existence of relationships between genetic diversity and environmental factors. The results showed that C. microphylla have high genetic diversity, and environmental gradients affected genetic diversity of C. microphylla populations. Genetic diversity of all populations was affected by many environmental factors and as well correlated with warm index and soil Olsen phosphorus (SOP) concentration. These results have important implications for restoration and management of these degraded ecosystems in arid and semi‐arid areas.
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Affiliation(s)
- Wenda Huang
- Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Lanzhou China
| | - Xueyong Zhao
- Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Lanzhou China
| | - Xin Zhao
- Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Lanzhou China
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Lanzhou China
| | - Jie Lian
- Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences Lanzhou China
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27
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Gilroy DL, van Oosterhout C, Komdeur J, Richardson DS. Toll-like receptor variation in the bottlenecked population of the endangered Seychelles warbler. Anim Conserv 2016. [DOI: 10.1111/acv.12307] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- D. L. Gilroy
- School of Biological Sciences; Norwich Research Park; University of East Anglia; Norwich UK
| | - C. van Oosterhout
- School of Environmental Sciences; Norwich Research Park; University of East Anglia; Norwich UK
| | - J. Komdeur
- Behavioural Ecology and Self-Organization; Centre for Ecological and Evolutionary Studies; University of Groningen; Groningen The Netherlands
| | - D. S. Richardson
- School of Biological Sciences; Norwich Research Park; University of East Anglia; Norwich UK
- Nature Seychelles; Mahe Republic of Seychelles
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28
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Di G, Miao X, Ke C, Kong X, Li H, You W. Protein changes in abalone foot muscle from three geographical populations of Haliotis diversicolor based on proteomic approach. Ecol Evol 2016; 6:3645-3657. [PMID: 27186366 PMCID: PMC4851958 DOI: 10.1002/ece3.2128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 12/25/2022] Open
Abstract
Using two‐dimensional gel electrophoresis, the foot muscle proteome of three geographical populations of Haliotis diversicolor were examined, with a total of 922 ± 21 protein spots detected in the Japanese population (JJ), 904 ± 25.6 in the Taiwanese population (TT), and 936 ± 16.2 in the Vietnamese population (VV). Of these, 254 spots showed differential expression and 85 protein spots percentage volumes varied more than twofold. Both “genotype” and “spot” analysis of variance approaches significantly showed differences among the three populations. Hierarchical clustering analysis showed that TT and VV clustered together followed by clustering with JJ, which is consistent with their geographical location. Following matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, 30 differentially expressed proteins involved in major biological processes including energy production and storage and stress response were identified. Of these proteins, proteins pertaining to muscle contraction and muscle protein regulation showed highest expression levels in VV samples. Proteins involved in energy production and storage, including ATP synthase beta subunit, fructose‐1,6‐bisphosphate aldolase, arginine kinase, enolase, triosephosphate isomerase, and tauropine dehydrogenase, showed diverse expression patterns among the three populations. For stress‐responsive proteins, the expression of heat shock protein 70 was JJ > VV > TT. The expression pattern of Cu/Zn‐superoxide dismutase was JJ > VV > TT. Overall, these results may aid in the detection of new differentially expressed proteins within three different abalone populations.
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Affiliation(s)
- Guilan Di
- College of Fisheries Henan Normal University Xinxiang 453007 China.,State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Xiulian Miao
- College of Life Sciences Liaocheng University Liaocheng 252059 China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Xianghui Kong
- College of Fisheries Henan Normal University Xinxiang 453007 China
| | - Hui Li
- College of Fisheries Henan Normal University Xinxiang 453007 China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen China
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29
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Hallingbäck HR, Fogelqvist J, Powers SJ, Turrion‐Gomez J, Rossiter R, Amey J, Martin T, Weih M, Gyllenstrand N, Karp A, Lagercrantz U, Hanley SJ, Berlin S, Rönnberg‐Wästljung A. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology. GLOBAL CHANGE BIOLOGY. BIOENERGY 2016; 8:670-685. [PMID: 27547245 PMCID: PMC4973673 DOI: 10.1111/gcbb.12280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/14/2015] [Indexed: 05/06/2023]
Abstract
Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).
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Affiliation(s)
- Henrik R. Hallingbäck
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Johan Fogelqvist
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Stephen J. Powers
- Computational and Systems Biology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | | | - Rachel Rossiter
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Joanna Amey
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Tom Martin
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Martin Weih
- Department of Crop Production EcologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Angela Karp
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala University752 36UppsalaSweden
| | - Steven J. Hanley
- AgroEcology DepartmentRothamsted ResearchHarpendenHertsAL5 2JQUK
| | - Sofia Berlin
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
| | - Ann‐Christin Rönnberg‐Wästljung
- Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural Sciences and Linnean Center for Plant BiologyP.O. Box 7043750 07UppsalaSweden
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30
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Duchemin SI, Glantz M, de Koning DJ, Paulsson M, Fikse WF. Identification of QTL on Chromosome 18 Associated with Non-Coagulating Milk in Swedish Red Cows. Front Genet 2016; 7:57. [PMID: 27148354 PMCID: PMC4832587 DOI: 10.3389/fgene.2016.00057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/25/2016] [Indexed: 11/19/2022] Open
Abstract
Non-coagulating (NC) milk, defined as milk not coagulating within 40 min after rennet-addition, can have a negative influence on cheese production. Its prevalence is estimated at 18% in the Swedish Red (SR) cow population. Our study aimed at identifying genomic regions and causal variants associated with NC milk in SR cows, by doing a GWAS using 777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21 herds in the south of Sweden, from which individual morning milk was sampled. NC milk was treated as a binary trait, receiving a score of one in case of non-coagulation within 40 min. For all 382 SR cows, 777k SNP genotypes were available as well as the combined genotypes of the genetic variants of αs1-β-κ-caseins. In addition, whole-genome sequences from the 1000 Bull Genome Consortium (Run 3) were available for 429 animals of 15 different breeds. From these sequences, 33 sequences belonged to SR and Finish Ayrshire bulls with a large impact in the SR cow population. Single-marker analyses were run in ASReml using an animal model. After fitting the casein loci, 14 associations at -Log10(P-value) > 6 identified a promising region located on BTA18. We imputed sequences to the 382 genotyped SR cows using Beagle 4 for half of BTA18, and ran a region-wide association study with imputed sequences. In a seven mega base-pairs region on BTA18, our strongest association with NC milk explained almost 34% of the genetic variation in NC milk. Since it is possible that multiple QTL are in strong LD in this region, 59 haplotypes were built, genetically differentiated by means of a phylogenetic tree, and tested in phenotype-genotype association studies. Haplotype analyses support the existence of one QTL underlying NC milk in SR cows. A candidate gene of interest is the VPS35 gene, for which one of our strongest association is an intron SNP in this gene. The VPS35 gene belongs to the mammary gene sets of pre-parturient and of lactating cows.
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Affiliation(s)
- Sandrine I. Duchemin
- Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
- Animal Breeding and Genomics Centre, Wageningen UniversityWageningen, Netherlands
| | - Maria Glantz
- Department of Food Technology, Engineering and Nutrition, Lund UniversityLund, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Marie Paulsson
- Department of Food Technology, Engineering and Nutrition, Lund UniversityLund, Sweden
| | - Willem F. Fikse
- Department of Animal Breeding and Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
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31
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Joost S, Negrini R, Milanesi E, Pellecchia M, Ajmone Marsan P, Consortium E. Detecting footprints of selection inOvis ariesby a spatial analysis approach. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2007.1s.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- S. Joost
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
| | - R. Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
| | - E. Milanesi
- Istituto di Zootecnia Generale, Università di Milano, Italy
| | - M. Pellecchia
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy
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32
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Evans SM, Sinclair EA, Poore AGB, Bain KF, Vergés A. Genotypic richness predicts phenotypic variation in an endangered clonal plant. PeerJ 2016; 4:e1633. [PMID: 26925313 PMCID: PMC4768672 DOI: 10.7717/peerj.1633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/06/2016] [Indexed: 11/20/2022] Open
Abstract
Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species. However, the strong link between genotypic and phenotypic variation suggests that a range of genotypes is still the best case scenario for adaptation to and recovery from predicted environmental change.
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Affiliation(s)
- Suzanna M Evans
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales, Australia; Evolution & Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Elizabeth A Sinclair
- School of Plant Biology and Oceans Institute, University of Western Australia, Perth, Western Australia, Australia; Science Directorate, Botanic Gardens and Parks Authority, West Perth Western Australia, Australia
| | - Alistair G B Poore
- Evolution & Ecology Research Centre, University of New South Wales , Sydney, New South Wales , Australia
| | - Keryn F Bain
- Evolution & Ecology Research Centre, University of New South Wales , Sydney, New South Wales , Australia
| | - Adriana Vergés
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales, Australia; Evolution & Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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33
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Heino M, Díaz Pauli B, Dieckmann U. Fisheries-Induced Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054339] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mikko Heino
- Department of Biology and Hjort Centre for Marine Ecosystem Dynamics, University of Bergen, N-5020 Bergen, Norway;
- Institute of Marine Research and Hjort Centre for Marine Ecosystem Dynamics, N-5817 Bergen, Norway
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria
| | - Beatriz Díaz Pauli
- Department of Biology and Hjort Centre for Marine Ecosystem Dynamics, University of Bergen, N-5020 Bergen, Norway;
| | - Ulf Dieckmann
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria
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34
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Hu YC, Kang CK, Tang CH, Lee TH. Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes. PLoS One 2015; 10:e0134959. [PMID: 26263550 PMCID: PMC4532362 DOI: 10.1371/journal.pone.0134959] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/16/2015] [Indexed: 12/20/2022] Open
Abstract
Milkfish (Chanos chanos), an important marine aquaculture species in southern Taiwan, show considerable euryhalinity but have low tolerance to sudden drops in water temperatures in winter. Here, we used high throughput next-generation sequencing (NGS) to identify molecular and biological processes involved in the responses to environmental changes. Preliminary tests revealed that seawater (SW)-acclimated milkfish tolerated lower temperatures than the fresh water (FW)-acclimated group. Although FW- and SW-acclimated milkfish have different levels of tolerance for hypothermal stress, to date, the molecular physiological basis of this difference has not been elucidated. Here, we performed a next-generation sequence analysis of mRNAs from four groups of milkfish. We obtained 29669 unigenes with an average length of approximately 1936 base pairs. Gene ontology (GO) analysis was performed after gene annotation. A large number of genes for molecular regulation were identified through a transcriptomic comparison in a KEGG analysis. Basal metabolic pathways involved in hypothermal tolerance, such as glycolysis, fatty acid metabolism, amino acid catabolism and oxidative phosphorylation, were analyzed using PathVisio and Cytoscape software. Our results indicate that in response to hypothermal stress, genes for oxidative phosphorylation, e.g., succinate dehydrogenase, were more highly up-regulated in SW than FW fish. Moreover, SW and FW milkfish used different strategies when exposed to hypothermal stress: SW milkfish up-regulated oxidative phosphorylation and catabolism genes to produce more energy budget, whereas FW milkfish down-regulated genes related to basal metabolism to reduce energy loss.
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Affiliation(s)
- Yau-Chung Hu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung, and Academia Sinica, Taipei, Taiwan
| | - Chao-Kai Kang
- Tainan Hydraulics Laboratory, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Hao Tang
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- * E-mail: (C-HT); (T-HL)
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
- * E-mail: (C-HT); (T-HL)
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Savage AE, Becker CG, Zamudio KR. Linking genetic and environmental factors in amphibian disease risk. Evol Appl 2015; 8:560-72. [PMID: 26136822 PMCID: PMC4479512 DOI: 10.1111/eva.12264] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/07/2015] [Indexed: 01/13/2023] Open
Abstract
A central question in evolutionary biology is how interactions between organisms and the environment shape genetic differentiation. The pathogen Batrachochytrium dendrobatidis (Bd) has caused variable population declines in the lowland leopard frog (Lithobates yavapaiensis); thus, disease has potentially shaped, or been shaped by, host genetic diversity. Environmental factors can also influence both amphibian immunity and Bd virulence, confounding our ability to assess the genetic effects on disease dynamics. Here, we used genetics, pathogen dynamics, and environmental data to characterize L. yavapaiensis populations, estimate migration, and determine relative contributions of genetic and environmental factors in predicting Bd dynamics. We found that the two uninfected populations belonged to a single genetic deme, whereas each infected population was genetically unique. We detected an outlier locus that deviated from neutral expectations and was significantly correlated with mortality within populations. Across populations, only environmental variables predicted infection intensity, whereas environment and genetics predicted infection prevalence, and genetic diversity alone predicted mortality. At one locality with geothermally elevated water temperatures, migration estimates revealed source-sink dynamics that have likely prevented local adaptation. We conclude that integrating genetic and environmental variation among populations provides a better understanding of Bd spatial epidemiology, generating more effective conservation management strategies for mitigating amphibian declines.
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Affiliation(s)
- Anna E Savage
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA ; Department of Biology, University of Central Florida 4110 Libra Drive, Orlando, FL 32816, USA
| | - Carlos G Becker
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA ; Department of Zoology, State University of Sao Paulo Av. 24A No. 1515, Rio Claro, SP 13506-900, Brazil
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA
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36
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Ozerov MY, Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J, Primmer CR, Vasemägi A. Generation of a neutral F
ST
baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin. J Evol Biol 2015; 28:1170-83. [DOI: 10.1111/jeb.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/17/2023]
Affiliation(s)
- M. Y. Ozerov
- Department of Biology; University of Turku; Turku Finland
| | - M. Himberg
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - T. Aykanat
- Department of Biology; University of Turku; Turku Finland
| | - D. S. Sendek
- State Research Institute on Lake and River Fisheries (GosNIORKh); St. Petersburg Russia
| | - H. Hägerstrand
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - A. Verliin
- Estonian Marine Institute; University of Tartu; Tartu Estonia
| | - T. Krause
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
| | - J. Olsson
- Department of Aquatic Resources; Institute for Coastal Research; Swedish University of Agricultural Sciences; Öregrund Sweden
| | - C. R. Primmer
- Department of Biology; University of Turku; Turku Finland
| | - A. Vasemägi
- Department of Biology; University of Turku; Turku Finland
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
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37
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Thanh NM, Jung H, Lyons RE, Njaci I, Yoon BH, Chand V, Tuan NV, Thu VTM, Mather P. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus). Mar Genomics 2015; 23:87-97. [PMID: 25979246 DOI: 10.1016/j.margen.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/03/2015] [Accepted: 05/03/2015] [Indexed: 12/17/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.
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Affiliation(s)
- Nguyen Minh Thanh
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia; Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Russell E Lyons
- Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia.
| | - Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Byoung-Ha Yoon
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejoen 305-333, Republic of Korea.
| | - Vincent Chand
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Nguyen Viet Tuan
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Vo Thi Minh Thu
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Peter Mather
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
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Vilas R, Vandamme SG, Vera M, Bouza C, Maes GE, Volckaert FAM, Martínez P. A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus). Mar Genomics 2015; 23:77-86. [PMID: 25959584 DOI: 10.1016/j.margen.2015.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/28/2015] [Accepted: 04/28/2015] [Indexed: 01/30/2023]
Abstract
Partitioning phenotypic variance in genotypic and environmental variance may benefit from the population genomic assignment of genes putatively involved in adaptation. We analyzed a total of 256 markers (120 microsatellites and 136 Single Nucleotide Polymorphisms - SNPs), several of them associated to Quantitative Trait Loci (QTL) for growth and resistance to pathologies, with the aim to identify potential adaptive variation in turbot Scophthalmus maximus L. The study area in the Northeastern Atlantic Ocean, from Iberian Peninsula to the Baltic Sea, involves a gradual change in temperature and an abrupt change in salinity conditions. We detected 27 candidate loci putatively under selection. At least four of the five SNPs identified as outliers are located within genes coding for ribosomal proteins or directly related with the production of cellular proteins. One of the detected outliers, previously identified as part of a QTL for growth, is a microsatellite linked to a gene coding for a growth factor receptor. A similar set of outliers was detected when natural populations were compared with a sample subjected to strong artificial selection for growth along four generations. The observed association between FST outliers and growth-related QTL supports the hypothesis of changes in growth as an adaptation to differences in temperature and salinity conditions. However, further work is needed to confirm this hypothesis.
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Affiliation(s)
- Román Vilas
- Departamento de Genética, Universidad de Santiago de Compostela, Facultad de Biología, Santiago de Compostela E-15706, Spain.
| | - Sara G Vandamme
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat 32, B-3000 Leuven, Belgium.
| | - Manuel Vera
- Departamento de Genética, Universidad de Santiago de Compostela, Facultad de Veterinaria, Lugo E-27002, Spain.
| | - Carmen Bouza
- Departamento de Genética, Universidad de Santiago de Compostela, Facultad de Veterinaria, Lugo E-27002, Spain.
| | - Gregory E Maes
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat 32, B-3000 Leuven, Belgium; Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, James Cook University, Townsville, 4811 QLD, Australia.
| | - Filip A M Volckaert
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat 32, B-3000 Leuven, Belgium.
| | - Paulino Martínez
- Departamento de Genética, Universidad de Santiago de Compostela, Facultad de Veterinaria, Lugo E-27002, Spain.
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Bitocchi E, Bellucci E, Rau D, Albertini E, Rodriguez M, Veronesi F, Attene G, Nanni L. European flint landraces grown in situ reveal adaptive introgression from modern maize. PLoS One 2015; 10:e0121381. [PMID: 25853809 PMCID: PMC4390310 DOI: 10.1371/journal.pone.0121381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/31/2015] [Indexed: 12/23/2022] Open
Abstract
We have investigated the role of selection in the determination of the detected levels of introgression from modern maize hybrid varieties into maize landraces still cultivated in situ in Italy. We exploited the availability of a historical collection of landraces undertaken before the introduction and widespread use of modern maize, to analyse genomic changes that have occurred in these maize landraces over 50 years of co-existence with hybrid varieties. We have combined a previously published SSR dataset (n=21) with an AFLP loci dataset (n=168) to provide higher resolution power and to obtain a more detailed picture. We show that selection pressures for adaptation have favoured new alleles introduced by migration from hybrids. This shows the potential for analysis of historical introgression even over this short period of 50 years, for an understanding of the evolution of the genome and for the identification of its functionally important regions. Moreover, this demonstrates that landraces grown in situ represent almost unique populations for use for such studies when the focus is on the domesticated plant. This is due to their adaptation, which has arisen from their dynamic evolution under a continuously changing agro-ecological environment, and their capture of new alleles from hybridisation. We have also identified loci for which selection has inhibited introgression from modern germplasm and has enhanced the distinction between landraces and modern maize. These loci indicate that selection acted in the past, during the formation of the flint and dent gene pools. In particular, the locus showing the strongest signals of selection is a Misfit transposable element. Finally, molecular characterisation of the same samples with two different molecular markers has allowed us to compare their performances. Although the genetic-diversity and population-structure analyses provide the same global qualitative pattern, which thus provides the same inferences, there are differences related to their natures and characteristics.
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Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Domenico Rau
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Monica Rodriguez
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Fabio Veronesi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Giovanna Attene
- Department of Agriculture, Università degli Studi di Sassari, Sassari, Italy
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Laaksonen T, Sirkiä PM, Calhim S, Brommer JE, Leskinen PK, Primmer CR, Adamík P, Artemyev AV, Belskii E, Both C, Bureš S, Burgess MD, Doligez B, Forsman JT, Grinkov V, Hoffmann U, Ivankina E, Král M, Krams I, Lampe HM, Moreno J, Mägi M, Nord A, Potti J, Ravussin PA, Sokolov L. Sympatric divergence and clinal variation in multiple coloration traits of Ficedula flycatchers. J Evol Biol 2015; 28:779-90. [PMID: 25683091 DOI: 10.1111/jeb.12604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/23/2015] [Accepted: 02/06/2015] [Indexed: 01/25/2023]
Abstract
Geographic variation in phenotypes plays a key role in fundamental evolutionary processes such as local adaptation, population differentiation and speciation, but the selective forces behind it are rarely known. We found support for the hypothesis that geographic variation in plumage traits of the pied flycatcher Ficedula hypoleuca is explained by character displacement with the collared flycatcher Ficedula albicollis in the contact zone. The plumage traits of the pied flycatcher differed strongly from the more conspicuous collared flycatcher in a sympatric area but increased in conspicuousness with increasing distance to there. Phenotypic differentiation (PST ) was higher than that in neutral genetic markers (FST ), and the effect of geographic distance remained when statistically controlling for neutral genetic differentiation. This suggests that a cline created by character displacement and gene flow explains phenotypic variation across the distribution of this species. The different plumage traits of the pied flycatcher are strongly to moderately correlated, indicating that they evolve non-independently from each other. The flycatchers provide an example of plumage patterns diverging in two species that differ in several aspects of appearance. The divergence in sympatry and convergence in allopatry in these birds provide a possibility to study the evolutionary mechanisms behind the highly divergent avian plumage patterns.
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Affiliation(s)
- T Laaksonen
- Department of Biology, University of Turku, Turku, Finland; Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Helsinki, Finland
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Ferrandiz-Rovira M, Bigot T, Allainé D, Callait-Cardinal MP, Cohas A. Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals? Heredity (Edinb) 2015; 114:485-93. [PMID: 25757407 DOI: 10.1038/hdy.2015.13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 01/19/2015] [Accepted: 01/23/2015] [Indexed: 11/10/2022] Open
Abstract
Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.
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Affiliation(s)
- M Ferrandiz-Rovira
- 1] Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France [2] Université Lyon, VetAgro Sup Campus Vet, Marcy-L'Étoile, France
| | - T Bigot
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
| | - D Allainé
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
| | - M-P Callait-Cardinal
- 1] Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France [2] Université Lyon, VetAgro Sup Campus Vet, Marcy-L'Étoile, France
| | - A Cohas
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
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Proteomic analysis of muscle between hybrid abalone and parental lines Haliotis gigantea Reeve and Haliotis discus hannai Ino. Heredity (Edinb) 2015; 114:564-74. [PMID: 25669609 DOI: 10.1038/hdy.2014.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 02/06/2023] Open
Abstract
To understand the potential molecular mechanism of heterosis, protein expression patterns were compared from hybrids of Haliotis gigantea (G) and Haliotis discus hannai (D) using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight analyses. Expression differences were observed in muscle samples from the four groups with 673±21.0 stained spots for H. discus hannai ♀ × H. discus hannai ♂ (DD), 692±25.6 for H. gigantea ♀ × H. gigantea ♂ (GG), 679±16.2 for H. discus hannai ♀ × H. gigantea ♂ (DG) (F1 hybrid) and 700±19 for H. gigantea ♀ × H. discus hannai ♂ (GD) (F1 hybrid). Different 2-DE image muscle protein spots had a mirrored relationship between purebreds and the F1 hybrid, suggesting that all stained spots in F1 hybrid muscle were on 2-DEs from parents. DD and DG clustered together first, and then clustered with GD, whereas the distance of DD and GG was maximal according to hierarchical cluster analysis. We identified 136 differentially expressed protein spots involved in major biological processes, including energy metabolism and stress response. Most energy metabolism proteins were additive, and stress-induced proteins displayed additivity or over-dominance. In these 136 identified protein spots, hybrid offspring with additivity or over-dominance accounted for 68.38%. Data show that a proteomic approach can provide functional prediction of abalone interspecific hybridization.
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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44
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Buehler D, Holderegger R, Brodbeck S, Schnyder E, Gugerli F. Validation of outlier loci through replication in independent data sets: a test on Arabis alpina. Ecol Evol 2014; 4:4296-306. [PMID: 25540691 PMCID: PMC4267868 DOI: 10.1002/ece3.1300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/11/2014] [Accepted: 10/01/2014] [Indexed: 12/25/2022] Open
Abstract
Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.
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Affiliation(s)
- Dominique Buehler
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Sabine Brodbeck
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Elvira Schnyder
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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Genetic differentiation and evolutionary adaptation in Cryptomeria japonica. G3-GENES GENOMES GENETICS 2014; 4:2389-402. [PMID: 25320072 PMCID: PMC4267934 DOI: 10.1534/g3.114.013896] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, FST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.
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Cullingham CI, Cooke JEK, Coltman DW. Cross-species outlier detection reveals different evolutionary pressures between sister species. THE NEW PHYTOLOGIST 2014; 204:215-229. [PMID: 24942459 PMCID: PMC4260136 DOI: 10.1111/nph.12896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/14/2014] [Indexed: 05/15/2023]
Abstract
Lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana) hybridize in western Canada, an area of recent mountain pine beetle range expansion. Given the heterogeneity of the environment, and indications of local adaptation, there are many unknowns regarding the response of these forests to future outbreaks. To better understand this we aim to identify genetic regions that have adaptive potential. We used data collected on 472 single nucleotide polymorphism (SNP) loci from 576 tree samples collected across 13 lodgepole pine-dominated sites and four jack pine-dominated sites. We looked at the relationship of genetic diversity with the environment, and we identified candidate loci using both frequency-based (arlequin and bayescan) and correlation-based (matsam and bayenv) methods. We found contrasting relationships between environmental variation and genetic diversity for the species. While we identified a number of candidate outliers (34 in lodgepole pine, 25 in jack pine, and 43 interspecific loci), we did not find any loci in common between lodgepole and jack pine. Many of the outlier loci identified were correlated with environmental variation. Using rigorous criteria we have been able to identify potential outlier SNPs. We have also found evidence of contrasting environmental adaptations between lodgepole and jack pine which could have implications for beetle spread risk.
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Affiliation(s)
- Catherine I Cullingham
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
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Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
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Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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Johnston SE, Orell P, Pritchard VL, Kent MP, Lien S, Niemelä E, Erkinaro J, Primmer CR. Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar). Mol Ecol 2014; 23:3452-68. [DOI: 10.1111/mec.12832] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FIN-20520 Finland
| | - Panu Orell
- Finnish Game and Fisheries Research Institute; Utsjoki FIN-99980 Finland
| | - Victoria L. Pritchard
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FIN-20520 Finland
| | - Matthew P. Kent
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences; Norwegian University of Life Sciences; Aas N-1432 Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences; Norwegian University of Life Sciences; Aas N-1432 Norway
| | - Eero Niemelä
- Finnish Game and Fisheries Research Institute; Utsjoki FIN-99980 Finland
| | - Jaakko Erkinaro
- Finnish Game and Fisheries Research Institute; Utsjoki FIN-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FIN-20520 Finland
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A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata. Gene 2014; 542:8-15. [DOI: 10.1016/j.gene.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 12/20/2013] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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Bradbury D, Smithson A, Krauss SL. Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations. Mol Ecol 2014; 22:5112-29. [PMID: 24118117 DOI: 10.1111/mec.12463] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/03/2013] [Accepted: 07/12/2013] [Indexed: 01/17/2023]
Abstract
Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.
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Affiliation(s)
- Donna Bradbury
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6005, Australia; Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, West Perth, WA 6009, Australia
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