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Bisht MS, Singh M, Chakraborty A, Sharma VK. Genome of the most noxious weed water hyacinth ( Eichhornia crassipes) provides insights into plant invasiveness and its translational potential. iScience 2024; 27:110698. [PMID: 39262811 PMCID: PMC11387899 DOI: 10.1016/j.isci.2024.110698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/07/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
The invasive character of Eichhornia crassipes (water hyacinth) is a major threat to global biodiversity and ecosystems. To investigate the genomic basis of invasiveness, we performed the genome and transcriptome sequencing of E. crassipes and reported the genome of 1.11 Gbp size with 63,299 coding genes and N50 of 1.98 Mb. We confirmed a recent whole genome duplication event in E. crassipes that resulted in high intraspecific collinearity and significant expansion in gene families. Further, the orthologs gene clustering analysis and comparative evolutionary analysis with 14 other aquatic invasive and non-invasive angiosperm species revealed adaptive evolution in genes associated with plant-pathogen interaction, hormone signaling, abiotic stress tolerance, heavy metals sequestration, photosynthesis, and cell wall biosynthesis with highly expanded gene families, which contributes toward invasive characteristics of the water hyacinth. However, these characteristics also make water hyacinth an excellent candidate for biofuel production, phytoremediation, and other translational applications.
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Affiliation(s)
- Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Mitali Singh
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
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2
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Giglio RM, Bowden CF, Brook RK, Piaggio AJ, Smyser TJ. Characterizing feral swine movement across the contiguous United States using neural networks and genetic data. Mol Ecol 2024; 33:e17489. [PMID: 39148259 DOI: 10.1111/mec.17489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
Globalization has led to the frequent movement of species out of their native habitat. Some of these species become highly invasive and capable of profoundly altering invaded ecosystems. Feral swine (Sus scrofa × domesticus) are recognized as being among the most destructive invasive species, with populations established on all continents except Antarctica. Within the United States (US), feral swine are responsible for extensive crop damage, the destruction of native ecosystems, and the spread of disease. Purposeful human-mediated movement of feral swine has contributed to their rapid range expansion over the past 30 years. Patterns of deliberate introduction of feral swine have not been well described as populations may be established or augmented through small, undocumented releases. By leveraging an extensive genomic database of 18,789 samples genotyped at 35,141 single nucleotide polymorphisms (SNPs), we used deep neural networks to identify translocated feral swine across the contiguous US. We classified 20% (3364/16,774) of sampled animals as having been translocated and described general patterns of translocation using measures of centrality in a network analysis. These findings unveil extensive movement of feral swine well beyond their dispersal capabilities, including individuals with predicted origins >1000 km away from their sampling locations. Our study provides insight into the patterns of human-mediated movement of feral swine across the US and from Canada to the northern areas of the US. Further, our study validates the use of neural networks for studying the spread of invasive species.
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Affiliation(s)
- Rachael M Giglio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Courtney F Bowden
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Ryan K Brook
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Timothy J Smyser
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
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3
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Sario S, Marques JP, Farelo L, Afonso S, Santos C, Melo-Ferreira J. Dissecting the invasion history of Spotted-Wing Drosophila (Drosophila suzukii) in Portugal using genomic data. BMC Genomics 2024; 25:813. [PMID: 39210249 PMCID: PMC11360492 DOI: 10.1186/s12864-024-10739-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The invasive pest Spotted-Wing Drosophila, Drosophila suzukii (Matsumura), causes extensive damage and production losses of soft-skinned fruits. Native to Asia, the species has now spread worldwide, with first reports in Portugal in 2012. In this study, we focus on the genomic signatures of the recent Portuguese invasion, in the context of worldwide patterns established in previous works. We analyzed whole genome pool sequencing data from three Portuguese populations (N = 240) sampled in 2019 and 2021. RESULTS The correlation of allele frequencies suggested that Portuguese populations are related to South European ones, indicating a Mediterranean invasion route. While two populations exhibited levels of genetic variation comparable to others in the invasive range, a third showed low levels of genetic diversity, which may result from a recent colonization of the region. Genome-wide analyses of natural selection identified ten genes previously associated with D. suzukii's invasive capacity, which may have contributed to the species' success in Portugal. Additionally, we pinpointed six genes evolving under positive selection across Portuguese populations but not in European ones, which is indicative of local adaptation. One of these genes, nAChRalpha7, encodes a nicotinic acetylcholine receptor, which are known targets for insecticides widely used for D. suzukii control, such as neonicotinoids and spinosyns. Although spinosyn resistance has been associated with mutations in the nAChRalpha6 in other Drosophila species, the putative role of nAChRalpha7 in insecticide resistance and local adaptation in Portuguese D. suzukii populations encourages future investigation. CONCLUSIONS Our results highlight the complex nature of rapid species invasions and the role of rapid local adaptation in determining the invasive capacity of these species.
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Affiliation(s)
- Sara Sario
- Biology Department, Faculty of Sciences, University of Porto, Porto, 4169-007, Portugal.
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, Porto, 4050-453, Portugal.
| | - João P Marques
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, 4485-661, Portugal
| | - Liliana Farelo
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, 4485-661, Portugal
| | - Sandra Afonso
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, 4485-661, Portugal
| | - Conceição Santos
- Biology Department, Faculty of Sciences, University of Porto, Porto, 4169-007, Portugal
- LAQV-REQUIMTE, Faculty of Sciences, University of Porto, Porto, 4050-453, Portugal
| | - José Melo-Ferreira
- Biology Department, Faculty of Sciences, University of Porto, Porto, 4169-007, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, 4485-661, Portugal
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4
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Galià-Camps C, Enguídanos A, Turon X, Pascual M, Carreras C. The past, the recent, and the ongoing evolutionary processes of the worldwide invasive ascidian Styela plicata. Mol Ecol 2024:e17502. [PMID: 39205460 DOI: 10.1111/mec.17502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Invasive species are one of the main threats to global biodiversity and, within marine ecosystems, tunicates feature some prominent examples. Styela plicata is an ascidian species inhabiting harbours in all temperate oceans and seas, thus being considered a thriving invasive species. However, this species' adaptive mechanisms, introduction history, and population structure have never been completely elucidated. Here, by genotyping 87 S. plicata individuals from 18 localities worldwide with 2b-RADseq, we confirm the global presence of four chromosome inversions, demonstrate population structuring on this species, detect local adaptation signals, and infer historical demographic events. We show that North Carolina individuals constitute an unrelated population, Atlanto-Mediterranean and Pacific localities form their own genetic clusters with substructuring, being the most evident the split between northern and southern Atlantic localities. The locality of South Carolina presents an intermediate genetic position between North Carolina and the other two groups pointing to a hybrid origin with recurrent gene flow. We generate and test demographic models, providing evidence of two independent introduction events to the Atlantic and Pacific, and an admixture that originated the population of South Carolina. Finally, we identify candidate loci for adaptation, with functions involved with cell processes, metabolism, development, and ion transport, among others. Overall, this study highlights the complex historical processes of S. plicata, which have led this species to its current distribution, population structure, and local adaptation footprint in oceans worldwide.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Spain
| | - Alba Enguídanos
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona (UB), Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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5
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Wang Z, Wang T, Zhang X, Wang J, Yang Y, Sun Y, Guo X, Wu Q, Nepovimova E, Watson AE, Kuca K. Biodiversity conservation in the context of climate change: Facing challenges and management strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173377. [PMID: 38796025 DOI: 10.1016/j.scitotenv.2024.173377] [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: 02/18/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
Biodiversity conservation amidst the uncertainty of climate change presents unique challenges that necessitate precise management strategies. The study reported here was aimed at refining understanding of these challenges and to propose specific, actionable management strategies. Employing a quantitative literature analysis, we meticulously examined 1268 research articles from the Web of Science database between 2005 and 2023. Through Cite Spaces and VOS viewer software, we conducted a bibliometric analysis and thematic synthesis to pinpoint emerging trends, key themes, and the geographical distribution of research efforts. Our methodology involved identifying patterns within the data, such as frequency of keywords, co-authorship networks, and citation analysis, to discern the primary focus areas within the field. This approach allowed us to distinguish between research concentration areas, specifically highlighting a predominant interest in Environmental Sciences Ecology (67.59 %) and Biodiversity Conservation (22.63 %). The identification of adaptive management practices and ecosystem services maintenance are central themes in the research from 2005 to 2023. Moreover, challenges such as understanding phenological shifts, invasive species dynamics, and anthropogenic pressures critically impact biodiversity conservation efforts. Our findings underscore the urgent need for precise, data-driven decision-making processes in the face of these challenges. Addressing the gaps identified, our study proposes targeted solutions, including the establishment of germplasm banks for at-risk species, the development of advanced genomic and microclimate models, and scenario analysis to predict and mitigate future conservation challenges. These strategies are aimed at enhancing the resilience of biodiversity against the backdrop of climate change through integrated, evidence-based approaches. By leveraging the compiled and analyzed data, this study offers a foundational framework for future research and practical action in biodiversity conservation strategies, demonstrating a path forward through detailed analysis and specified solutions.
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Affiliation(s)
- Zhirong Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Tongxin Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Xiujuan Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China.
| | - Junbang Wang
- National Ecosystem Science Data Center, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yongsheng Yang
- The Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining 810001, China
| | - Yu Sun
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Xiaohua Guo
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Qinghua Wu
- College Life Science, Yangtze University, Jingzhou 434025, China; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove 500 03, Czech Republic
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove 500 03, Czech Republic
| | - Alan E Watson
- National Ecosystem Science Data Center, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove 500 03, Czech Republic.
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McEvoy SL, Meyer RS, Hasenstab-Lehman KE, Guilliams CM. The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California. G3 (BETHESDA, MD.) 2024; 14:jkae117. [PMID: 38845594 PMCID: PMC11304951 DOI: 10.1093/g3journal/jkae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/26/2024] [Indexed: 08/09/2024]
Abstract
We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTRs) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99% were functionally annotated. BUSCO scores for the annotated proteins were 96.0% complete of which 77.6% was single copy and 18.4% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.
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Affiliation(s)
- Susan L McEvoy
- Department of Conservation and Research, Santa Barbara Botanic Garden, Santa Barbara, CA 93105, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - C Matt Guilliams
- Department of Conservation and Research, Santa Barbara Botanic Garden, Santa Barbara, CA 93105, USA
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7
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North HL, Fu Z, Metz R, Stull MA, Johnson CD, Shirley X, Crumley K, Reisig D, Kerns DL, Gilligan T, Walsh T, Jiggins CD, Sword GA. Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea. Mol Biol Evol 2024; 41:msae129. [PMID: 38941083 PMCID: PMC11259193 DOI: 10.1093/molbev/msae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
Insect crop pests threaten global food security. This threat is amplified through the spread of nonnative species and through adaptation of native pests to control measures. Adaptations such as pesticide resistance can result from selection on variation within a population, or through gene flow from another population. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has evolved resistance to a wide range of pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid-resistance gene CYP337B3 to South American H. zea via adaptive introgression. To understand whether this could contribute to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites. We report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4 Mbp region containing CYP337B3. Next, we identify signatures of selection in the panmictic population of nonadmixed H. zea, identifying a selective sweep at a second cytochrome P450 gene: CYP333B3. We estimate that its derived allele conferred a ∼5% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Overall, we document two mechanisms of rapid adaptation: the introduction of fitness-enhancing alleles through interspecific introgression, and selection on intraspecific variation.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Zhen Fu
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Richard Metz
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Matt A Stull
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Charles D Johnson
- AgriLife Genomics and Bioinformatics Service, Texas A&M University, College Station, TX 77843, USA
| | - Xanthe Shirley
- Animal and Plant Health Inspection Service, United States Department of Agriculture, College Station, TX, USA
| | - Kate Crumley
- Agrilife Extension, Texas A&M University, Wharton, TX, USA
| | - Dominic Reisig
- Department of Entomology and Plant Pathology, North Carolina State University, Plymouth, NC, 27962, USA
| | - David L Kerns
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Todd Gilligan
- Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO, USA
| | - Tom Walsh
- Black Mountain Laboratories, Commonwealth Scientific and Industrial Research Organization, Canberra, Australia
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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8
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Khattak WA, Sun J, Hameed R, Zaman F, Abbas A, Khan KA, Elboughdiri N, Akbar R, He F, Ullah MW, Al-Andal A, Du D. Unveiling the resistance of native weed communities: insights for managing invasive weed species in disturbed environments. Biol Rev Camb Philos Soc 2024; 99:753-777. [PMID: 38174626 DOI: 10.1111/brv.13043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024]
Abstract
Weed communities influence the dynamics of ecosystems, particularly in disturbed environments where anthropogenic activities often result in higher pollution. Understanding the dynamics existing between native weed communities and invasive species in disturbed environments is crucial for effective management and normal ecosystem functioning. Recognising the potential resistance of native weed communities to invasion in disturbed environments can help identify suitable native plants for restoration operations. This review aims to investigate the adaptations exhibited by native and non-native weeds that may affect invasions within disturbed environments. Factors such as ecological characteristics, altered soil conditions, and adaptations of native weed communities that potentially confer a competitive advantage relative to non-native or invasive weeds in disturbed environments are analysed. Moreover, the roles of biotic interactions such as competition, mutualistic relationships, and allelopathy in shaping the invasion resistance of native weed communities are described. Emphasis is given to the consideration of the resistance of native weeds as a key factor in invasion dynamics that provides insights for conservation and restoration efforts in disturbed environments. Additionally, this review underscores the need for further research to unravel the underlying mechanisms and to devise targeted management strategies. These strategies aim to promote the resistance of native weed communities and mitigate the negative effects of invasive weed species in disturbed environments. By delving deeper into these insights, we can gain an understanding of the ecological dynamics within disturbed ecosystems and develop valuable insights for the management of invasive species, and to restore long-term ecosystem sustainability.
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Affiliation(s)
- Wajid Ali Khattak
- School of Emergency Management, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
| | - Jianfan Sun
- School of Emergency Management, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, PO Box 215009, Suzhou City, Jiangsu Province, P.R. China
| | - Rashida Hameed
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
| | - Fawad Zaman
- Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, Jiangxi Agricultural University, PO Box 330045, Nanchang City, Jiangxi Province, P.R. China
- Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, PO Box 330045, Nanchang City, Jiangxi Province, P.R. China
| | - Adeel Abbas
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
| | - Khalid Ali Khan
- Applied College, Center of Bee Research and its Products, Unit of Bee Research and Honey Production, and Research Center for Advanced Materials Science (RCAMS), King Khalid University, PO Box 9004, Abha, 61413, Saudi Arabia
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, PO Box 2440, Ha'il, 81441, Saudi Arabia
- Chemical Engineering Process Department, National School of Engineers Gabes, University of Gabes, 6029, Gabes, Tunisia
| | - Rasheed Akbar
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
- Department of Entomology, The University of Haripur, PO Box 22620, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Feng He
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of The Environmental and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
| | - Abeer Al-Andal
- Department of Biology, College of Science, King Khalid University, PO Box 960, Abha, 61413, Saudi Arabia
| | - Daolin Du
- School of the Environment and Safety Engineering, Jiangsu University, No. 301, Xuefu Road, PO Box 212013, Zhenjiang City, Jiangsu Province, China
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9
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Barmentlo NWG, Meirmans PG, Stiver WH, Yarkovich JG, McCann BE, Piaggio AJ, Wright D, Smyser TJ, Bosse M. Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States. Mol Ecol 2024; 33:e17383. [PMID: 38747342 DOI: 10.1111/mec.17383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.
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Affiliation(s)
- Niek W G Barmentlo
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Blake E McCann
- Theodore Roosevelt National Park, Medora, North Dakota, USA
| | | | - Dominic Wright
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Timothy J Smyser
- USDA APHIS WS National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Mirte Bosse
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wageningen University & Research - Animal Breeding and Genomics, Wageningen, The Netherlands
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10
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Dai JX, Cao LJ, Chen JC, Yang F, Shen XJ, Ma LJ, Hoffmann AA, Chen M, Wei SJ. Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm. Mol Ecol 2024; 33:e17038. [PMID: 37277936 DOI: 10.1111/mec.17038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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Affiliation(s)
- Jin-Xu Dai
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Min Chen
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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11
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Navarro JM, Cárdenas L, Ortiz A, Figueroa Á, Morley SA, Vargas-Chacoff L, Leclerc JC, Détrée C. Testing the physiological capacity of the mussel Mytilus chilensis to establish into the Southern Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170941. [PMID: 38360303 DOI: 10.1016/j.scitotenv.2024.170941] [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: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
The Southern Ocean and the Antarctic Circumpolar Current create environmental conditions that serve as an efficient barrier to prevent the colonization of non-native species (NNS) in the marine ecosystems of Antarctica. However, warming of the Southern Ocean and the increasing number of transport opportunities are reducing the physiological and physical barriers, increasing the chances of NNS arriving. The aim of this study was to determine the limits of survival of the juvenile mussels, M. chilensis, under current Antarctic conditions and those projected under climate change. These assessments were used to define the mussels potential for establishment in the Antarctic region. Experimental mussels were exposed to four treatments: -1.5 °C (Antarctic winter), 2 °C (Antarctic summer), 4 °C (Antarctic projected) and 8 °C (control) for 80 days and a combination of physiological and transcriptomics approaches were used to investigate mussel response. The molecular responses of mussels were congruent with the physiological results, revealing tolerance to Antarctic winter temperatures. However, a higher number of regulated differentially expressed gene (DEGs) were reported in mussels exposed to Antarctic winter temperatures (-1.5 °C). This tolerance was associated with the activation of the biological processes associated with apoptosis (up regulated) and both cell division and cilium assembly (down regulated). The reduced feeding rate and the negative scope for growth, for a large part of the exposure period at -1.5 °C, suggests that Antarctic winter temperatures represents an environmental barrier to M. chilensis from the Magellanic region settling in the Antarctic. Although M. chilensis are not robust to current Antarctica thermal conditions, future warming scenarios are likely to weaken these physiological barriers. These results strongly suggest that the West Antarctic Peninsula could become part of Mytilus distributional range, especially with dispersal aided by increasing maritime transport activity across the Southern Ocean.
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Affiliation(s)
- Jorge M Navarro
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile.
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro Ortiz
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile
| | - Álvaro Figueroa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Simon A Morley
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile; Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral d Chile, Valdivia, Chile
| | - Jean-Charles Leclerc
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Camille Détrée
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA) Université de Caen-Normandie, CREC marine station, 54 rue du Docteur Charcot, 14530 Luc-sur-mer, France
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12
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Nardi F, Boschi S, Funari R, Cucini C, Cardaioli E, Potter D, Asano SI, Toubarro D, Meier M, Paoli F, Carapelli A, Frati F. The direction, timing and demography of Popillia japonica (Coleoptera) invasion reconstructed using complete mitochondrial genomes. Sci Rep 2024; 14:7120. [PMID: 38531924 DOI: 10.1038/s41598-024-57667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
The Japanese beetle Popillia japonica is a pest insect that feeds on hundreds of species of wild and cultivated plants including important fruit, vegetable, and field crops. Native to Japan, the pest has invaded large areas of the USA, Canada, the Azores (Portugal), Italy, and Ticino (Switzerland), and it is considered a priority for control in the European Union. We determined the complete mitochondrial genome sequence in 86 individuals covering the entire distribution of the species. Phylogenetic analysis supports a major division between South Japan and Central/North Japan, with invasive samples coming from the latter. The origin of invasive USA samples is incompatible, in terms of the timing of the event, with a single introduction, with multiple Japanese lineages having been introduced and one accounting for most of the population expansion locally. The origin of the two invasive European populations is compatible with two different invasions followed by minimal differentiation locally. Population analyses provide the possibility to estimate the rate of sequence change from the data and to date major invasion events. Demographic analysis identifies a population expansion followed by a period of contraction prior to the invasion. The present study adds a time and demographic dimension to available reconstructions.
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Affiliation(s)
- Francesco Nardi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy.
| | - Sara Boschi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Rebecca Funari
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Claudio Cucini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Elena Cardaioli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Daniel Potter
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Shin-Ichiro Asano
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Duarte Toubarro
- Biotechnology Centre of Azores, University of the Azores, Ponta Delgada, Portugal
| | - Michela Meier
- Servizio fitosanitario cantonale, Dipartimento delle finanze e dell'economia, Bellinzona, Switzerland
| | - Francesco Paoli
- Council for Agricultural Research and Agricultural Economy Analysis (CREA), Florence, Italy
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy
| | - Francesco Frati
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- BAT-Center, Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, Portici, Italy
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13
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Dogantzis KA, Raffiudin R, Putra RE, Shaleh I, Conflitti IM, Pepinelli M, Roberts J, Holmes M, Oldroyd BP, Zayed A, Gloag R. Post-invasion selection acts on standing genetic variation despite a severe founding bottleneck. Curr Biol 2024; 34:1349-1356.e4. [PMID: 38428415 DOI: 10.1016/j.cub.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/12/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Invasive populations often have lower genetic diversity relative to the native-range populations from which they derive.1,2 Despite this, many biological invaders succeed in their new environments, in part due to rapid adaptation.3,4,5,6 Therefore, the role of genetic bottlenecks in constraining the adaptation of invaders is debated.7,8,9,10 Here, we use whole-genome resequencing of samples from a 10-year time-series dataset, representing the natural invasion of the Asian honey bee (Apis cerana) in Australia, to investigate natural selection occurring in the aftermath of a founding event. We find that Australia's A. cerana population was founded by as few as one colony, whose arrival was followed by a period of rapid population expansion associated with an increase of rare variants.11 The bottleneck resulted in a steep loss of overall genetic diversity, yet we nevertheless detected loci with signatures of positive selection during the first years post-invasion. When we investigated the origin of alleles under selection, we found that selection acted primarily on the variation introduced by founders and not on the variants that arose post-invasion by mutation. In all, our data highlight that selection on standing genetic variation can occur in the early years post-invasion, even where founding bottlenecks are severe.
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Affiliation(s)
- Kathleen A Dogantzis
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Rika Raffiudin
- IPB University, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor 16680, Indonesia
| | - Ramadhani Eka Putra
- Bandung Institute of Technology, School of Life Sciences and Technology, Bandung 40132, West Java, Indonesia
| | - Ismail Shaleh
- IPB University, Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor 16680, Indonesia
| | - Ida M Conflitti
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Mateus Pepinelli
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - John Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Michael Holmes
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Benjamin P Oldroyd
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia
| | - Amro Zayed
- York University, Department of Biology, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.
| | - Rosalyn Gloag
- University of Sydney, School of Life and Environmental Sciences, Sydney, NSW 2006, Australia.
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14
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Ma LJ, Cao LJ, Chen JC, Tang MQ, Song W, Yang FY, Shen XJ, Ren YJ, Yang Q, Li H, Hoffmann AA, Wei SJ. Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect. Mol Biol Evol 2024; 41:msae044. [PMID: 38401527 PMCID: PMC10924284 DOI: 10.1093/molbev/msae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.
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Affiliation(s)
- Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Meng-Qing Tang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fang-Yuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Ya-Jing Ren
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiong Yang
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ary Anthony Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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15
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Zhang S, Song F, Wang J, Li X, Zhang Y, Zhou W, Xu L. Gut microbiota facilitate adaptation of invasive moths to new host plants. THE ISME JOURNAL 2024; 18:wrae031. [PMID: 38423525 PMCID: PMC10980833 DOI: 10.1093/ismejo/wrae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Gut microbiota are important in the adaptation of phytophagous insects to their plant hosts. However, the interaction between gut microbiomes and pioneering populations of invasive insects during their adaptation to new hosts, particularly in the initial phases of invasion, has been less studied. We studied the contribution of the gut microbiome to host adaptation in the globally recognized invasive pest, Hyphantria cunea, as it expands its range into southern China. The southern population of H. cunea shows effective adaptation to Metasequoia glyptostroboides and exhibits greater larval survival on Metasequoia than the original population. Genome resequencing revealed no significant differences in functions related to host adaptation between the two populations. The compatibility between southern H. cunea populations and M. glyptostroboides revealed a correlation between the abundance of several gut bacteria genera (Bacteroides, Blautia, and Coprococcus) and H. cunea survival. Transplanting the larval gut microbiome from southern to northern populations enhanced the adaptability of the latter to the previously unsuitable plant M. glyptostroboides. This research provides evidence that the gut microbiome of pioneering populations can enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.
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Affiliation(s)
- Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Feng Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jie Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiayu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yuxin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenwu Zhou
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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16
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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17
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Hofmeister NR, Stuart KC, Warren WC, Werner SJ, Bateson M, Ball GF, Buchanan KL, Burt DW, Cardilini APA, Cassey P, De Meyer T, George J, Meddle SL, Rowland HM, Sherman CDH, Sherwin WB, Vanden Berghe W, Rollins LA, Clayton DF. Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions. Mol Ecol 2023. [PMID: 37933429 DOI: 10.1111/mec.17195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
| | - Katarina C Stuart
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wesley C Warren
- Department of Animal Sciences and Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Melissa Bateson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gregory F Ball
- Department of Psychology, University of Maryland, College Park, Maryland, USA
| | | | - David W Burt
- Office of the Deputy Vice-Chancellor (Research and Innovation), The University of Queensland, Brisbane, Queensland, Australia
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam P A Cardilini
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia
| | - Phillip Cassey
- Invasion Science & Wildlife Ecology Lab, University of Adelaide, Adelaide, South Australia, Australia
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Julia George
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Simone L Meddle
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Hannah M Rowland
- Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Craig D H Sherman
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - William B Sherwin
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University Antwerp, Antwerp, Belgium
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Evolution & Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - David F Clayton
- Department of Genetics & Biochemistry, Clemson University, Clemson, South Carolina, USA
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18
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Zhao X, Zheng T, Gao T, Song N. Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations. BMC Genomics 2023; 24:547. [PMID: 37715145 PMCID: PMC10503073 DOI: 10.1186/s12864-023-09652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. RESULTS To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. CONCLUSIONS Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China
| | - Tianlun Zheng
- Zhejiang Fisheries Technical Extension Center, Hangzhou, 310023, Zhejiang, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, Shandong, China.
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19
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Sparks MM, Schraidt CE, Yin X, Seeb LW, Christie MR. Rapid genetic adaptation to a novel ecosystem despite a large founder event. Mol Ecol 2023. [PMID: 37668092 DOI: 10.1111/mec.17121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72-a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.
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Affiliation(s)
- Morgan M Sparks
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Claire E Schraidt
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Xiaoshen Yin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
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20
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Vaughan AL, Parvizi E, Matheson P, McGaughran A, Dhami MK. Current stewardship practices in invasion biology limit the value and secondary use of genomic data. Mol Ecol Resour 2023. [PMID: 37647021 DOI: 10.1111/1755-0998.13858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/09/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an 'undescribed' sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis-such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.
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Affiliation(s)
- Amy L Vaughan
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
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21
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Crossman CA, Fontaine MC, Frasier TR. A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales. Mol Ecol 2023. [PMID: 37577945 DOI: 10.1111/mec.17099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent- and identity-by-descent-based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne ) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome-wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome-wide datasets to help resolve long-standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long-term small Ne , low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps.
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Affiliation(s)
- Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 224), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Timothy R Frasier
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada
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22
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Matheson P, Parvizi E, Fabrick JA, Siddiqui HA, Tabashnik BE, Walsh T, McGaughran A. Genome-wide analysis reveals distinct global populations of pink bollworm (Pectinophora gossypiella). Sci Rep 2023; 13:11762. [PMID: 37474628 PMCID: PMC10359307 DOI: 10.1038/s41598-023-38504-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
The pink bollworm (Pectinophora gossypiella) is one of the world's most destructive pests of cotton. This invasive lepidopteran occurs in nearly all cotton-growing countries. Its presence in the Ord Valley of North West Australia poses a potential threat to the expanding cotton industry there. To assess this threat and better understand population structure of pink bollworm, we analysed genomic data from individuals collected in the field from North West Australia, India, and Pakistan, as well as from four laboratory colonies that originated in the United States. We identified single nucleotide polymorphisms (SNPs) using a reduced-representation, genotyping-by-sequencing technique (DArTseq). The final filtered dataset included 6355 SNPs and 88 individual genomes that clustered into five groups: Australia, India-Pakistan, and three groups from the United States. We also analysed sequences from Genbank for mitochondrial DNA (mtDNA) locus cytochrome c oxidase I (COI) for pink bollworm from six countries. We found low genetic diversity within populations and high differentiation between populations from different continents. The high genetic differentiation between Australia and the other populations and colonies sampled in this study reduces concerns about gene flow to North West Australia, particularly from populations in India and Pakistan that have evolved resistance to transgenic insecticidal cotton. We attribute the observed population structure to pink bollworm's narrow host plant range and limited dispersal between continents.
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Affiliation(s)
- Paige Matheson
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand.
| | - Elahe Parvizi
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
| | - Jeffrey A Fabrick
- United States Department of Agriculture Agricultural Research Service, United States Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | | | - Bruce E Tabashnik
- Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA
| | - Tom Walsh
- Commonwealth Scientific Industrial Research Organisation Environment, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Angela McGaughran
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
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23
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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24
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Li H, Peng Y, Wang Y, Summerhays B, Shu X, Vasquez Y, Vansant H, Grenier C, Gonzalez N, Kansagra K, Cartmill R, Sujii ER, Meng L, Zhou X, Lövei GL, Obrycki JJ, Sethuraman A, Li B. Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird. BMC Biol 2023; 21:141. [PMID: 37337183 DOI: 10.1186/s12915-023-01638-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research. RESULTS Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits. CONCLUSIONS Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.
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Affiliation(s)
- Hongran Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, People's Republic of China
| | - Yansong Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bryce Summerhays
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | - Xiaohan Shu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yumary Vasquez
- Department of Biological Sciences, California State University, San Marcos, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Hannah Vansant
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | - Christy Grenier
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | - Nicolette Gonzalez
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | - Khyati Kansagra
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | - Ryan Cartmill
- Department of Biological Sciences, California State University, San Marcos, CA, USA
| | | | - Ling Meng
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Gábor L Lövei
- Department of Agroecology, Flakkebjerg Research Centre, Aarhus University, Aarhus, Denmark
- ELKH-DE Anthropocene Ecology Research Group, University of Debrecen, Debrecen, Hungary
- Department of Zoology & Ecology, Hungarian University of Agriculture & Life Sciences, Godollo, Hungary
| | - John J Obrycki
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Arun Sethuraman
- Department of Biological Sciences, California State University, San Marcos, CA, USA.
- Department of Biology, San Diego State University, San Diego, CA, USA.
| | - Baoping Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China.
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25
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Irimia RE, Montesinos D, Chaturvedi A, Sanders I, Hierro JL, Sotes G, Cavieres LA, Eren Ö, Lortie CJ, French K, Brennan AC. Trait evolution during a rapid global weed invasion despite little genetic differentiation. Evol Appl 2023; 16:997-1011. [PMID: 37216028 PMCID: PMC10197227 DOI: 10.1111/eva.13548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 05/24/2023] Open
Abstract
Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (F ST), and comparing it with phenotypic differentiation (P ST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non-native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non-native ranges. The native versus invasive P ST-F ST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non-native populations.
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Affiliation(s)
- Ramona E. Irimia
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Plant Evolutionary Ecology, Institute of Evolution and EcologyUniversity of TübingenTübingenGermany
| | - Daniel Montesinos
- Centre for Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraPortugal
- Australian Tropical HerbariumJames Cook UniversityQueenslandCairnsAustralia
| | - Anurag Chaturvedi
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Ian Sanders
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - José L. Hierro
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, UNLPamSanta RosaArgentina
| | - Gastón Sotes
- Laboratorio de Ecología, Biogeografía y Evolución Vegetal (LEByEV), Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad Nacional de La Pampa (UNLPam)Santa RosaArgentina
| | - Lohengrin A. Cavieres
- Departamento de Botánica, Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Instituto de Ecología y Biodiversidad (IEB)SantiagoChile
| | - Özkan Eren
- Aydın Adnan Menderes Üniversitesi, Biyoloji Bölümü, Fen‐Edebiyat FakültesiAydınTurkey
| | - Christopher J. Lortie
- Department of BiologyYork UniversityOntarioTorontoCanada
- The National Center for Ecological Analysis and Synthesis (NCEAS), UCSBCaliforniaUSA
| | - Kristine French
- School of Earth, Atmospheric and Life SciencesUniversity of WollongongNew South WalesWollongongAustralia
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26
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Qi S, Wang J, Zhang Y, Naz M, Afzal MR, Du D, Dai Z. Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091860. [PMID: 37176919 PMCID: PMC10181282 DOI: 10.3390/plants12091860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.
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Affiliation(s)
- Shanshan Qi
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yi Zhang
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Zhicong Dai
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
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27
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Favreau E, Cini A, Taylor D, Câmara Ferreira F, Bentley MA, Cappa F, Cervo R, Privman E, Schneider J, Thiéry D, Mashoodh R, Wyatt CDR, Brown RL, Bodrug-Schepers A, Stralis-Pavese N, Dohm JC, Mead D, Himmelbauer H, Guigo R, Sumner S. Putting hornets on the genomic map. Sci Rep 2023; 13:6232. [PMID: 37085574 PMCID: PMC10121689 DOI: 10.1038/s41598-023-31932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/20/2023] [Indexed: 04/23/2023] Open
Abstract
Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.
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Affiliation(s)
- Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Alessandro Cini
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, Università di Pisa, Via Volta 6, 56126, Pisa, Italy
| | - Daisy Taylor
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Michael A Bentley
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Federico Cappa
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Rita Cervo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Abba Hushi 199, 3498838, Haifa, Israel
| | - Jadesada Schneider
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Denis Thiéry
- INRAe, UMR 1065 Santé et Agroécologie du Vignoble, Bordeaux Sciences Agro, ISVV, Université de Bordeaux, 33883, Villenave d'Ornon, France
| | - Rahia Mashoodh
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher D R Wyatt
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Robert L Brown
- Manaaki Whenua - Landcare Research, 54 Gerald Street, Lincoln, 7608, New Zealand
| | - Alexandrina Bodrug-Schepers
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Nancy Stralis-Pavese
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Daniel Mead
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Roderic Guigo
- Centre for Genomic Regulation, Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
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Beesley A, Whibley A, Santure AW, Battles HT. The introduction and distribution history of the common myna ( Acridotheres tristis) in New Zealand. NEW ZEALAND JOURNAL OF ZOOLOGY 2023. [DOI: 10.1080/03014223.2023.2182332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Affiliation(s)
- Annika Beesley
- Anthropology, School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W. Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Heather T. Battles
- Anthropology, School of Social Sciences, University of Auckland, Auckland, New Zealand
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Barrett CF, Corbett CW, Thixton-Nolan HL. A lack of population structure characterizes the invasive Lonicera japonica in West Virginia and across eastern North America. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530604. [PMID: 36909462 PMCID: PMC10002767 DOI: 10.1101/2023.03.01.530604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, and the ubiquity of invasive species across the landscape make them highly accessible for studies of invasion history and population dynamics associated with their introduction, establishment, spread, and ecological interactions. Here we focus on Lonicera japonica, one of the most damaging invasive vine species in North America. We leveraged digitized collections data and contemporary field collections to reconstruct the invasion history and characterize patterns of genomic variation in the eastern USA, using a straightforward method for generating nucleotide polymorphism data and a recently published, chromosome-level genome for the species. We found an overall lack of population structure among sites in northern West Virginia, USA, as well as across sites in the central and eastern USA. Heterozygosity and population differentiation were both low based on Fst, analysis of molecular variance, principal components analysis, and cluster-based analyses. We also found evidence of high inbreeding coefficients and significant linkage disequilibrium, in line with the ability of this otherwise outcrossing, perennial species to propagate vegetatively. Our findings corroborate earlier studies based on allozyme data, and suggest that intentional, human-assisted spread explains the lack of population structure, as this species was planted for erosion control and as an ornamental, escaping cultivation repeatedly across the USA. Finally, we discuss how plant invasion genomics can be incorporated into experiential undergraduate education as a way to integrate teaching and research.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Cameron W. Corbett
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Hana L. Thixton-Nolan
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
| | - Biology 320 Class
- Department of Biology, West Virginia University, 5209 Life Sciences Building, 53 Campus Drive, Morgantown, WV, USA 26506
- Biology 320 Capstone Students, “Total Science Experience: Genomics” [Appendix 1]
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Barrett CF, Ramachandran D, Chen CH, Corbett CW, Huebner CD, Sinn BT, Yu WB, Suetsugu K. Mitochondrial genome sequencing and analysis of the invasive Microstegium vimineum: a resource for systematics, invasion history, and management. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527995. [PMID: 36798355 PMCID: PMC9934601 DOI: 10.1101/2023.02.10.527995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Premise of the Research Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes), due to the difficulty in assembly with short-read technology. Invasive species lag behind crops and other economically important species in this respect, representing a lack of tools for management and land conservation efforts. Methodology The mitogenome of Microstegium vimineum, one of the most damaging invasive plant species in North America, was sequenced and analyzed using long-read data, providing a resource for biologists and managers. We conducted analyses of genome content, phylogenomic analyses among grasses and relatives based on mitochondrial coding regions, and an analysis of mitochondrial single nucleotide polymorphism in this invasive grass species. Pivotal Results The assembly is 478,010 bp in length and characterized by two large, inverted repeats, and a large, direct repeat. However, the genome could not be circularized, arguing against a "master circle" structure. Long-read assemblies with data subsets revealed several alternative genomic conformations, predominantly associated with large repeats. Plastid-like sequences comprise 2.4% of the genome, with further evidence of Class I and Class II transposable element-like sequences. Phylogenetic analysis placed M. vimineum with other Microstegium species, excluding M. nudum, but with weak support. Analysis of polymorphic sites across 112 accessions of M. vimineum from the native and invasive ranges revealed a complex invasion history. Conclusions We present an in-depth analysis of mitogenome structure, content, phylogenetic relationships, and range-wide genomic variation in M. vimineum's invasive US range. The mitogenome of M. vimineum is typical of other andropogonoid grasses, yet mitochondrial sequence variation across the invasive and native ranges is extensive. Our findings suggest multiple introductions to the US over the last century, with subsequent spread, secondary contact, long-distance dispersal, and possibly post-invasion selection on awn phenotypes. Efforts to produce genomic resources for invasive species, including sequenced mitochondrial genomes, will continue to provide tools for their effective management, and to help predict and prevent future invasions.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Dhanushya Ramachandran
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Chih-Hui Chen
- Endemic Species Research Institute, 1 Ming-Sheng East Road, Jiji, Nantou 552, Taiwan
| | - Cameron W. Corbett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Cynthia D. Huebner
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
- USDA Forest Service, Northern Research Station, 180 Canfield Street, Morgantown, West Virginia, USA 26505
- Division of Plant and Soil Sciences, West Virginia University, 204 Evansdale Greenhouse, Morgantown, West Virginia, USA 26506
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, 1 South Grove Street, Westerville, OH USA 43081
- Faculty of Biology, University of Latvia, 1 Jelgavas iela, Riga, Latvia LV-1004
| | - Wen-Bin Yu
- Center for Integrative Conservation Xishuangbanna Tropical Botanical Garden, CAS Mengla, Yunnan 666303, China
| | - Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
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Touchard F, Simon A, Bierne N, Viard F. Urban rendezvous along the seashore: Ports as Darwinian field labs for studying marine evolution in the Anthropocene. Evol Appl 2023; 16:560-579. [PMID: 36793678 PMCID: PMC9923491 DOI: 10.1111/eva.13443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022] Open
Abstract
Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic is not predicted to fade in the coming decades. Ports share common characteristics: Species find themselves in novel singular environments, with particular abiotic properties-e.g., pollutants, shading, protection from wave action-within novel communities in a melting pot of invasive and native taxa. Here, we discuss how this drives evolution, including setting up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps, however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining "biological portuarization," defined as the repeated evolution of marine species in port ecosystems under human-altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks and so provide replicated life-size evolutionary experiments essential to support predictive evolutionary sciences.
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Affiliation(s)
| | - Alexis Simon
- ISEM, EPHE, IRDUniversité MontpellierMontpellierFrance
- Center of Population Biology and Department of Evolution and EcologyUniversity of California DavisDavisCaliforniaUSA
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32
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Global invasion history and native decline of the common starling: insights through genetics. Biol Invasions 2023. [DOI: 10.1007/s10530-022-02982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
AbstractFew invasive birds are as globally successful as the Common or European Starling (Sturnus vulgaris). Native to the Palearctic, the starling has been intentionally introduced to North and South America, South Africa, Australia, and the Pacific Islands, enabling us to explore species traits that may contribute to its invasion success. Coupling the rich studies of life history and more recent explorations of genomic variation among invasions, we illustrate how eco-evolutionary dynamics shape the invasion success of this long-studied and widely distributed species. Especially informative is the comparison between Australian and North American invasions, because these populations colonized novel ranges concurrently and exhibit shared signals of selection despite distinct population histories. In this review, we describe population dynamics across the native and invasive ranges, identify putatively selected traits that may influence the starling’s spread, and suggest possible determinants of starling success world-wide. We also identify future opportunities to utilize this species as a model for avian invasion research, which will inform our understanding of species’ rapid evolution in response to environmental change.
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Parvizi E, Dhami MK, Yan J, McGaughran A. Population genomic insights into invasion success in a polyphagous agricultural pest, Halyomorpha halys. Mol Ecol 2023; 32:138-151. [PMID: 36261398 PMCID: PMC10099481 DOI: 10.1111/mec.16740] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/07/2023]
Abstract
Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we used genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated single nucleotide polymorphisms (SNPs) located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has probably evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such traits, highlighting the need for future sustainable and targeted management strategies.
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Affiliation(s)
- Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
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34
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Cohen ZP, François O, Schoville SD. Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation. Integr Comp Biol 2022; 62:1827-1837. [PMID: 36036479 DOI: 10.1093/icb/icac137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 01/05/2023] Open
Abstract
Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA.,Insect Control and Cotton Disease Research Unit, USDA, Agricultural Research Service, College Station, TX, USA
| | | | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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35
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Leonhardt F, Arranz Aveces C, Müller A, Angin B, Jegu M, Haynes P, Ernst R. Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges. NEOBIOTA 2022. [DOI: 10.3897/neobiota.79.86778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is no clear empirical evidence to support the general assumption that genetic diversity favours successful invasions. Many invading species disperse and establish successfully despite low genetic diversity, a phenomenon known as the genetic paradox of biological invasion. Model systems that allow comparison of genetic patterns between exotic and native source populations are still scarce. This is particularly true for amphibians. Here we compare genetic patterns of the widely introduced Johnstone’s Whistling Frog, Eleutherodactylus johnstonei, with its successful alien congener E. antillensis and the single island endemic E. portoricensis. Genetic diversity and population differentiation in native and introduced populations of the three taxa were inferred from mitochondrial D-loop sequences (235 bp). Our results reveal that exotic populations of the two alien taxa, E. johnstonei and E. antillensis, are not only genetically impoverished due to founder effects, but that, moreover, their native range source-populations exhibit low genetic diversity and inter-population differentiation in the first place. Populations of the endemic E. portoricensis, on the other hand, are genetically more diverse and show marked inter-population differentiation. These observed genetic patterns are consistent with geological processes and invasion histories. We argue that the establishment success of the alien taxa in our model system is better explained by ecological factors and anthropogenic drivers than by genetic diversity. As these factors provide more parsimonious explanations, they should be given priority in management decisions. However, molecular studies with higher resolution are needed to fully test possible genetic and epigenetic components that could promote the invasion process.
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36
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Poveda-Martínez D, Salinas NA, Aguirre MB, Sánchez-Restrepo AF, Hight S, Díaz-Soltero H, Logarzo G, Hasson E. Genomic and ecological evidence shed light on the recent demographic history of two related invasive insects. Sci Rep 2022; 12:19629. [PMID: 36385480 PMCID: PMC9669014 DOI: 10.1038/s41598-022-21548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Hypogeococcus pungens is a species complex native to southern South America that is composed of at least five putative species, each one specialized in the use of different host plants. Two of these undescribed species were registered as invasive in Central and North America: Hyp-C is a cactophagous mealybug that became an important pest that threatens endemic cactus species in Puerto Rico, and Hyp-AP feeds on Amaranthaceae and Portulacaceae hosts, but does not produce severe damage to the host plants. We quantified genomic variation and investigated the demographic history of both invasive species by means of coalescent-based simulations using high throughput sequencing data. We also evaluated the incidence of host plant infestation produced by both species and used an ecological niche modeling approach to assess potential distribution under current and future climatic scenarios. Our genetic survey evinced the footprints of strong effective population size reduction and signals of genetic differentiation among populations within each species. Incidence of plant attacks varied between species and among populations within species, with some host plant species preferred over others. Ecological niche modeling suggested that under future climatic scenarios both species would expand their distribution ranges in Puerto Rico. These results provide valuable information for the design of efficient management and control strategies of the Puerto Rican cactus pest and shed light on the evolutionary pathways of biological invasions.
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Affiliation(s)
- Daniel Poveda-Martínez
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina.
- Facultad de Ciencias Exactas Y Naturales, Instituto de Ecología Genética Y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nicolas A Salinas
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Belén Aguirre
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina.
| | - Andrés F Sánchez-Restrepo
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Stephen Hight
- Insect Behavior and Biocontrol Research Unit (IBBRU), USDA-ARS, Tallahassee, FL, USA
| | | | - Guillermo Logarzo
- Fundación Para El Estudio de Especies Invasivas (FuEDEI), Hurlingham, Argentina
| | - Esteban Hasson
- Facultad de Ciencias Exactas Y Naturales, Instituto de Ecología Genética Y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Cohen ZP, Chen YH, Groves R, Schoville SD. Evidence of hard-selective sweeps suggests independent adaptation to insecticides in Colorado potato beetle (Coleoptera: Chrysomelidae) populations. Evol Appl 2022; 15:1691-1705. [PMID: 36330305 PMCID: PMC9624080 DOI: 10.1111/eva.13498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 12/01/2022] Open
Abstract
Pesticide resistance provides one of the best examples of rapid evolution to environmental change. The Colorado potato beetle (CPB) has a long and noteworthy history as a super-pest due to its ability to repeatedly develop resistance to novel insecticides and rapidly expand its geographic and host plant range. Here, we investigate regional differences in demography, recombination, and selection using whole-genome resequencing data from two highly resistant CPB populations in the United States (Hancock, Wisconsin and Long Island, New York). Demographic reconstruction corroborates historical records for a single pest origin during the colonization of the Midwestern and Eastern United States in the mid- to late-19th century and suggests that the effective population size might be higher in Long Island, NY than Hancock, WI despite contemporary potato acreage of Wisconsin being far greater. Population-based recombination maps show similar background recombination rates between these populations, as well as overlapping regions of low recombination that intersect with important metabolic detoxification genes. In both populations, we find compelling evidence for hard selective sweeps linked to insecticide resistance with multiple sweeps involving genes associated with xenobiotic metabolism, stress response, and defensive chemistry. Notably, only two candidate insecticide resistance genes are shared among both populations, but both appear to be independent hard selective sweep events. This suggests that repeated, rapid, and independent evolution of genes may underlie CPB's pest status among geographically distinct populations.
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Affiliation(s)
- Zachary P. Cohen
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Yolanda H. Chen
- Department of Plant and Soil SciencesUniversity of VermontBurlingtonVermontUSA
| | - Russell Groves
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Sean D. Schoville
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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Lan T, Li H, Yang S, Shi M, Han L, Sahu SK, Lu Y, Wang J, Zhou M, Liu H, Huang J, Wang Q, Zhu Y, Wang L, Xu Y, Lin C, Liu H, Hou Z. The chromosome-scale genome of the raccoon dog: Insights into its evolutionary characteristics. iScience 2022; 25:105117. [PMID: 36185367 PMCID: PMC9523411 DOI: 10.1016/j.isci.2022.105117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanchun Xu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518120, China
- Corresponding author
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Corresponding author
| | - Zhijun Hou
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
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Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci Rep 2022; 12:13987. [PMID: 35977991 PMCID: PMC9385848 DOI: 10.1038/s41598-022-17937-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/03/2022] [Indexed: 11/14/2022] Open
Abstract
Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy and providing new insights into the genetic factors that underpin invasion success compared to research based on a small number of genetic loci. We examine the extent to which population genomic resources, including reference genomes, have been used or are available for invasive species research. We find that 82% of species on the International Union for Conservation of Nature “100 Worst Invasive Alien Species” list have been studied using some form of population genetic data, but just 32% of these species have been studied using population genomic data. Further, 55% of the list’s species lack a reference genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate invasion is critical, but despite a promising trend of increasing uptake, “invasion genomics” is still in its infancy. We discuss how population genomic data can enhance our understanding of biological invasion and inform proactive detection and management of invasive species, and we call for more research that specifically targets this area.
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40
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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41
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McGaughran A, Mori E, Quilodrán CS. Editorial: The Genomics of Biological Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.810817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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42
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Taylor RS, Jensen EL, Coltman DW, Foote AD, Lamichhaney S. Seeing the whole picture: What molecular ecology is gaining from whole genomes. Mol Ecol 2021; 30:5917-5922. [PMID: 34845797 DOI: 10.1111/mec.16282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Biology Department, Western University, London, Ontario, Canada
| | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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43
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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44
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Ramachandran D, Huebner CD, Daly M, Haimovitz J, Swale T, Barrett CF. Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum). Genome Biol Evol 2021; 13:6413638. [PMID: 34718556 PMCID: PMC8598173 DOI: 10.1093/gbe/evab238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12-Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long-terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 Myr, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.
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Affiliation(s)
| | - Cynthia D Huebner
- Department of Biology, West Virginia University, USA.,USDA Forest Service, Northern Research Station, Morgantown, West Virginia, USA
| | - Mark Daly
- Dovetail Genomics, LLC, Scotts Valley, California, USA
| | | | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, California, USA
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45
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Foote AD, Hooper R, Alexander A, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Excoffier L, Martin SLF, Forney KA, Gerrodette T, Gilbert MTP, Guinet C, Hanson MB, Li S, Martin MD, Robertson KM, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Wolf JBW, Fan G, Zhang Y, Morin PA. Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Mol Ecol 2021; 30:6162-6177. [PMID: 34416064 DOI: 10.1111/mec.16137] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
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Affiliation(s)
- Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK.,CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca Hooper
- University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Alana Alexander
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Charles Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Jay Barlow
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - John W Durban
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Sarah L Fordyce Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Karin A Forney
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, California, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Tim Gerrodette
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Guinet
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Filipa I P Samarra
- University of Iceland's Institute of Research Centres, Vestmannaeyjar, Iceland
| | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK.,Cetacean Research Program, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Paul Tixier
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France.,MARBEC Université de Montpellier-CNRS-IFREMER-IRD, Sète, France
| | | | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington, USA
| | - Jochen B W Wolf
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Translational Immunology group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
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