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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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Zhang J, Xu C, Wang S, Wang S, Li Y. Variations in Genetic Diversity of Invasive Species Lithobates catesbeianus in China. Animals (Basel) 2024; 14:1287. [PMID: 38731291 PMCID: PMC11083970 DOI: 10.3390/ani14091287] [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: 03/27/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.
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Affiliation(s)
- Jiaqi Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China; (J.Z.); (C.X.); (S.W.); (S.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China; (J.Z.); (C.X.); (S.W.); (S.W.)
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China; (J.Z.); (C.X.); (S.W.); (S.W.)
| | - Siqi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China; (J.Z.); (C.X.); (S.W.); (S.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China; (J.Z.); (C.X.); (S.W.); (S.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
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3
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Sarre SD, Adamack AT, Hitchen Y, Soulsbury CD, Gruber B, Berry OF. The genetic signature left by the range expansion of red foxes in Australia is detectable after more than 80 years of population stability. Ecol Evol 2024; 14:e11212. [PMID: 38584770 PMCID: PMC10994981 DOI: 10.1002/ece3.11212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Reconstructing biological invasions from historical sources can provide insights into how they occur but are difficult to do when invasions are poorly documented. Genetic signatures left by invaders can also offer insights into invasion routes, points of origin and general biology but often present conclusions that are contradictory to expectations. Here, we test the ability of continental-wide microsatellite genotype data from 29 loci and 3122 samples to reconstruct the well-documented invasion of red foxes Vulpes vulpes from the United Kingdom into Australia over 150 years ago, an invasion that has led to the extinction of many native species. Our analysis reveals several key signals of invasion evident in Australian foxes. They display lower levels of diversity than foxes sampled from the UK, exhibit clines in diversity from the point of introduction (south-east Australia) to the edge of their range, and show strong evidence of allele surfing in westerly and north-easterly directions. These characteristics are consistent with a single point of origin followed by rapid expansion in westerly and north-easterly directions as suggested by historical records. We also find little genetic structure in foxes across Australia with only the vast Nullarbor Plains and Great Victoria Desert region presenting a detectable barrier to their dispersal. As such, no mainland region within the current range of foxes can be considered genetically isolated and therefore appropriate for localised eradication efforts. Overall, our analyses demonstrate the ability of comprehensive population genetic studies to reconstruct invasion histories even after more than 80 years since colonisation was stabilised.
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Affiliation(s)
- Stephen D. Sarre
- Centre for Conservation Ecology and Genomics, Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Aaron T. Adamack
- Centre for Conservation Ecology and Genomics, Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
- Science Branch, Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Yvette Hitchen
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- Helix Molecular SolutionsLeedervilleWestern AustraliaAustralia
| | - Carl D. Soulsbury
- School of Life & Environmental SciencesUniversity of LincolnLincolnUK
| | - Bernd Gruber
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Oliver F. Berry
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- National Collections and Marine Infrastructure, CSIRO, Indian Ocean Marine Research CentreThe University of Western AustraliaCrawleyWestern AustraliaAustralia
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Dort EN, Layne E, Feau N, Butyaev A, Henrissat B, Martin FM, Haridas S, Salamov A, Grigoriev IV, Blanchette M, Hamelin RC. Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits. Sci Rep 2023; 13:17203. [PMID: 37821494 PMCID: PMC10567782 DOI: 10.1038/s41598-023-44005-w] [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: 04/04/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.
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Affiliation(s)
- E N Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - E Layne
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - N Feau
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - A Butyaev
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - B Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - F M Martin
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Université de Lorraine, Champenoux, France
| | - S Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - A Salamov
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - M Blanchette
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - R C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada.
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Williams GM, Ginzel MD, Ma Z, Adams DC, Campbell F, Lovett GM, Pildain MB, Raffa KF, Gandhi KJK, Santini A, Sniezko RA, Wingfield MJ, Bonello P. The Global Forest Health Crisis: A Public-Good Social Dilemma in Need of International Collective Action. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:377-401. [PMID: 37253697 DOI: 10.1146/annurev-phyto-021722-024626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Society is confronted by interconnected threats to ecological sustainability. Among these is the devastation of forests by destructive non-native pathogens and insects introduced through global trade, leading to the loss of critical ecosystem services and a global forest health crisis. We argue that the forest health crisis is a public-good social dilemma and propose a response framework that incorporates principles of collective action. This framework enables scientists to better engage policymakers and empowers the public to advocate for proactive biosecurity and forest health management. Collective action in forest health features broadly inclusive stakeholder engagement to build trust and set goals; accountability for destructive pest introductions; pooled support for weakest-link partners; and inclusion of intrinsic and nonmarket values of forest ecosystems in risk assessment. We provide short-term and longer-term measures that incorporate the above principles to shift the societal and ecological forest health paradigm to a more resilient state.
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Affiliation(s)
- Geoffrey M Williams
- International Programs, US Forest Service, US Department of Agriculture, Lansing, Michigan, USA;
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Matthew D Ginzel
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - Zhao Ma
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Damian C Adams
- Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Faith Campbell
- Center for Invasive Species Prevention, Bethesda, Maryland, USA
| | - Gary M Lovett
- Cary Institute of Ecosystem Studies, Millbrook, New York, USA
| | - María Belén Pildain
- Centro de Investigación y Extensión Forestal Andino Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Esquel, Chubut, Argentina
| | - Kenneth F Raffa
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kamal J K Gandhi
- D. B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council, Sesto Fiorentino, Italy
| | - Richard A Sniezko
- Dorena Genetic Resource Center, US Forest Service, US Department of Agriculture, Cottage Grove, Oregon, USA
| | - Michael J Wingfield
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Pierluigi Bonello
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA;
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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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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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8
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Bracalini M, Benigno A, Aglietti C, Panzavolta T, Moricca S. Thousand Cankers Disease in Walnut Trees in Europe: Current Status and Management. Pathogens 2023; 12:pathogens12020164. [PMID: 36839436 PMCID: PMC9959596 DOI: 10.3390/pathogens12020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Thousand cankers disease (TCD) is a new deadly disease in walnut trees (Juglans spp.), which is plaguing commercial plantations, natural groves, and ornamental black walnut trees (Juglans nigra) in their native and invasion areas in the US and, more recently, in artificial plantations and amenity trees in the newly-invaded areas in Europe (Italy). This insect/fungus complex arises from the intense trophic activity of the bark beetle vector Pityophthorus juglandis in the phloem of Juglans spp. and the subsequent development of multiple Geosmithia morbida cankers around beetles' entry/exit holes. After an analysis of the main biological and ecological traits of both members of this insect/fungus complex, this review explores the options available for TCD prevention and management. Special focus is given to those diagnostic tools developed for disease detection, surveillance, and monitoring, as well as to existing phytosanitary regulations, protocols, and measures that comply with TCD eradication and containment. Only integrated disease management can effectively curtail the pervasive spread of TCD, thus limiting the damage to natural ecosystems, plantations, and ornamental walnuts.
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9
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Picq S, Wu Y, Martemyanov VV, Pouliot E, Pfister SE, Hamelin R, Cusson M. Range‐wide population genomics of the spongy moth,
Lymantria dispar
(Erebidae): Implications for biosurveillance, subspecies classification and phylogeography of a destructive moth. Evol Appl 2023; 16:638-656. [PMID: 36969137 PMCID: PMC10033852 DOI: 10.1111/eva.13522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
The spongy moth, Lymantria dispar, is an irruptive forest pest native to Eurasia where its range extends from coast to coast and overspills into northern Africa. Accidentally introduced from Europe in Massachusetts in 1868-1869, it is now established in North America where it is considered a highly destructive invasive pest. A fine-scale characterization of its population genetic structure would facilitate identification of source populations for specimens intercepted during ship inspections in North America and would enable mapping of introduction pathways to help prevent future incursions into novel environments. In addition, detailed knowledge of L. dispar's global population structure would provide new insight into the adequacy of its current subspecies classification system and its phylogeographic history. To address these issues, we generated >2000 genotyping-by-sequencing-derived SNPs from 1445 contemporary specimens sampled at 65 locations in 25 countries/3 continents. Using multiple analytical approaches, we identified eight subpopulations that could be further partitioned into 28 groups, achieving unprecedented resolution for this species' population structure. Although reconciliation between these groupings and the three currently recognized subspecies proved to be challenging, our genetic data confirmed circumscription of the japonica subspecies to Japan. However, the genetic cline observed across continental Eurasia, from L. dispar asiatica in East Asia to L. d. dispar in Western Europe, points to the absence of a sharp geographical boundary (e.g., the Ural Mountains) between these two subspecies, as suggested earlier. Importantly, moths from North America and the Caucasus/Middle East displayed high enough genetic distances from other populations to warrant their consideration as separate subspecies of L. dispar. Finally, in contrast with earlier mtDNA-based investigations that identified the Caucasus as L. dispar's place of origin, our analyses suggest continental East Asia as its evolutionary cradle, from where it spread to Central Asia and Europe, and to Japan through Korea.
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Affiliation(s)
- Sandrine Picq
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
| | - Yunke Wu
- United States Department of Agriculture, APHIS, PPQ, Science and Technology Forest Pest Methods Laboratory Massachusetts Buzzards Bay USA
- Department of Ecology and Evolutionary Biology Cornell University New York Ithaca USA
| | - Vyacheslav V. Martemyanov
- Institute of Systematics and Ecology of Animals SB RAS Novosibirsk Russia
- Biological Institute National Research Tomsk State University Tomsk Russia
| | - Esther Pouliot
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
| | - Scott E. Pfister
- United States Department of Agriculture, APHIS, PPQ, Science and Technology Forest Pest Methods Laboratory Massachusetts Buzzards Bay USA
| | - Richard Hamelin
- Department of Forest and Conservation Sciences The University of British Columbia British Columbia Vancouver Canada
| | - Michel Cusson
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
- Département de biochimie, de microbiologie et de bio‐informatique Université Laval Quebec Quebec City Canada
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10
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Feau N, Herath P, Hamelin RC. DNA-Barcoding Identification of Plant Pathogens for Disease Diagnostics. Methods Mol Biol 2023; 2659:37-49. [PMID: 37249883 DOI: 10.1007/978-1-0716-3159-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The accurate identification of plant pathogens is a critical step to prevent their spread and attenuate their impact. Among the wide range of methods available, DNA-barcoding, i.e., the identification of an organism through the PCR amplification and sequencing of a single locus, remains one of the most straightforward and accurate plant-pathogen identification techniques that can be used in a generic molecular biology lab. This chapter provides a detailed protocol for the isolation of genomic DNA of fungal and oomycete pathogens from fresh field samples and the amplification and sequencing of the internal transcribed spacer (ITS) locus for DNA-barcoding purpose. Amendments to the protocol are provided to help in resolving issues related to the analysis of complicated samples and to the lack of species resolution that can be encountered with ITS barcodes.
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Affiliation(s)
- Nicolas Feau
- Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Victoria, BC, Canada.
| | - Padmini Herath
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Richard C Hamelin
- Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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11
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Independent Evolution Has Led to Distinct Genomic Signatures in Dutch Elm Disease-Causing Fungi and Other Vascular Wilts-Causing Fungal Pathogens. J Fungi (Basel) 2022; 9:jof9010002. [PMID: 36675823 PMCID: PMC9864908 DOI: 10.3390/jof9010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Vascular wilts are important diseases caused by plant pathogenic fungi that result in the rapid death of their plant hosts. This is due to a systemic defense mechanism whereby the plant induces the compartmentalization of the infected vascular system in order to reduce the propagation of the fungus. The ascomycete class Sordariomycetes contains several species that cause vascular wilts in diverse plant hosts, and they can be classified into four taxonomic orders. The genetic mechanisms of pathogenesis have already been investigated in Fusarium and Verticillium species, but they have not yet been compared with other well-known wilt-causing species, especially fungi causing oak wilt or Dutch elm disease (DED). Here we analyzed 20 whole genome assemblies of wilt-causing fungi together with 56 other species using phylogenetic approaches to trace expansions and contractions of orthologous gene families and gene classes related to pathogenicity. We found that the wilt-causing pathogens evolved seven times, experiencing the largest fold changes in different classes of genes almost every time. However, some similarities exist across groups of wilt pathogens, particularly in Microascales and Ophiostomatales, and these include the common gains and losses of genes that make up secondary metabolite clusters (SMC). DED pathogens do not experience large-scale gene expansions, with most of the gene classes, except for some SMC families, reducing in number. We also found that gene family expansions in the most recent common ancestors of wilt pathogen groups are enriched for carbohydrate metabolic processes. Our study shows that wilt-causing species evolve primarily through distinct changes in their repertoires of pathogenicity-related genes and that there is the potential importance of carbohydrate metabolism genes for regulating osmosis in those pathogens that penetrate the plant vascular system.
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12
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Tobin PC, Robinet C. Advances in understanding and predicting the spread of invading insect populations. CURRENT OPINION IN INSECT SCIENCE 2022; 54:100985. [PMID: 36216241 DOI: 10.1016/j.cois.2022.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Understanding and predicting the spread of invading insects is a critical challenge in management programs that aim to minimize ecological and economic harm to native ecosystems. Although efforts to quantify spread rates have been well studied over the past several decades, opportunities to improve our ability to estimate rates of spread, and identify the factors, such as habitat suitability and climate, that influence spread, remain. We review emerging sources of data that can be used to delineate distributional boundaries through time and thus serve as a basis for quantifying spread rates. We then address advances in modeling methods that facilitate our understanding of factors that drive invasive insect spread. We conclude by highlighting some remaining challenges in understanding and predicting invasive insect spread, such as the role of climate change and biotic similarity between the native and introduced ranges, particularly as it applies to decision-making in management programs.
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Affiliation(s)
- Patrick C Tobin
- University of Washington, School of Environmental and Forest Sciences, 123 Anderson Hall, 3715 W. Stevens Way NE, Seattle, WA, USA.
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13
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Cox MP, Guo Y, Winter DJ, Sen D, Cauldron NC, Shiller J, Bradley EL, Ganley AR, Gerth ML, Lacey RF, McDougal RL, Panda P, Williams NM, Grunwald NJ, Mesarich CH, Bradshaw RE. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Front Microbiol 2022; 13:1038444. [PMID: 36406440 PMCID: PMC9667082 DOI: 10.3389/fmicb.2022.1038444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2023] Open
Abstract
Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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Affiliation(s)
- Murray P. Cox
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J. Winter
- Institute of Environmental Science and Research (ESR), Porirua, New Zealand
| | | | - Nicholas C. Cauldron
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | | | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Austen R. Ganley
- School of Biological Sciences and Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Monica L. Gerth
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Randy F. Lacey
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | | | | | - Niklaus J. Grunwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, OR, United States
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand,*Correspondence: Rosie E. Bradshaw,
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14
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The fast invasion of Europe by the box tree moth: an additional example coupling multiple introduction events, bridgehead effects and admixture events. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02887-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIdentifying the invasion routes of non-native species is crucial to understanding invasions and customizing management strategies. The box tree moth, Cydalima perspectalis, is native to Asia and was recently accidentally introduced into Europe as a result of the ornamental plant trade. Over the last 15 years, it has spread across the continent and has reached the Caucasus and Iran. It is threatening Buxus trees in both urban areas and forests. To investigate the species’ invasion routes, native and invasive box tree moth populations were sampled, and moth’s genetic diversity and structure were compared using microsatellite markers. Our approximate Bayesian computation analyses strongly suggest that invasion pathways were complex. Primary introductions originating from eastern China probably occurred independently twice in Germany and once in the Netherlands. There were also possibly bridgehead effects, where at least three invasive populations may have served as sources for other invasive populations within Europe, with indication of admixture between the two primary invasive populations. The bridgehead populations were likely those in the countries that play a major role in the ornamental plant trade in Europe, notably Germany, the Netherlands, and Italy. All these invasion processes likely facilitated its fast expansion across Europe and illustrate the role played by the ornamental plant trade not only in the moth’s introduction from China but also in the species’ spread across Europe, leading to an invasion with a complex pattern.
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15
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Hao R, Liu Y, Shen W, Zhao R, Jiang B, Song H, Yan M, Ma H. Surveillance of emerging infectious diseases for biosecurity. SCIENCE CHINA LIFE SCIENCES 2022; 65:1504-1516. [PMID: 35287183 PMCID: PMC8918423 DOI: 10.1007/s11427-021-2071-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022]
Abstract
Emerging infectious diseases, such as COVID-19, continue to pose significant threats to human beings and their surroundings. In addition, biological warfare, bioterrorism, biological accidents, and harmful consequences arising from dual-use biotechnology also pose a challenge for global biosecurity. Improving the early surveillance capabilities is necessary for building a common biosecurity shield for the global community of health for all. Furthermore, surveillance could provide early warning and situational awareness of biosecurity risks. However, current surveillance systems face enormous challenges, including technical shortages, fragmented management, and limited international cooperation. Detecting emerging biological risks caused by unknown or novel pathogens is of particular concern. Surveillance systems must be enhanced to effectively mitigate biosecurity risks. Thus, a global strategy of meaningful cooperation based on efficient integration of surveillance at all levels, including interdisciplinary integration of techniques and interdepartmental integration for effective management, is urgently needed. In this paper, we review the biosecurity risks by analyzing potential factors at all levels globally. In addition to describing biosecurity risks and their impact on global security, we also focus on analyzing the challenges to traditional surveillance and propose suggestions on how to integrate current technologies and resources to conduct effective global surveillance.
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Affiliation(s)
- Rongzhang Hao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Yuqi Liu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Wanzhu Shen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Bo Jiang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, China
| | - Hongbin Song
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China.
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China.
| | - Muyang Yan
- The First Medical Center of PLA General Hospital, Beijing, 100853, China.
| | - Hui Ma
- The Nursing Department of PLA General Hospital, Beijing, 100853, China.
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16
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Cui M, Wu Y, Javal M, Giguère I, Roux G, Andres JA, Keena M, Shi J, Wang B, Braswell E, Pfister SE, Hamelin R, Roe A, Porth I. Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky). Evol Appl 2022; 15:934-953. [PMID: 35782014 PMCID: PMC9234632 DOI: 10.1111/eva.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Human-assisted movement has allowed the Asian longhorned beetle (ALB, Anoplophora glabripennis (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6102 single-nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped 712 individuals from ALB's native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.
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Affiliation(s)
- Mingming Cui
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Yunke Wu
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Marion Javal
- Centre d'Écologie Fonctionnelle et ÉvolutiveUniversité MontpellierMontpellierFrance
| | - Isabelle Giguère
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Géraldine Roux
- Institut National de la Recherche AgronomiqueUR633 Zoologie ForestièreOrléansFrance
- COSTUniversité d’OrléansOrléansFrance
| | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Melody Keena
- United States Department of AgricultureForest ServiceNorthern Research StationHamdenConnecticutUSA
| | - Juan Shi
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
| | - Baode Wang
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Evan Braswell
- Insect Management and Molecular Diagnostics LaboratoryPlant Protection and Quarantine Science and Technology, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureEdinburgTexasUSA
| | - Scott E. Pfister
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Richard Hamelin
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
- Department of Forest and Conservation SciencesThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Amanda Roe
- Canadian Forest ServiceGreat Lakes Forestry CentreNatural Resources CanadaSault Ste. MarieOntarioCanada
| | - Ilga Porth
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
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17
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Hamelin RC, Bilodeau GJ, Heinzelmann R, Hrywkiw K, Capron A, Dort E, Dale AL, Giroux E, Kus S, Carleson NC, Grünwald NJ, Feau N. Genomic biosurveillance detects a sexual hybrid in the sudden oak death pathogen. Commun Biol 2022; 5:477. [PMID: 35589982 PMCID: PMC9120034 DOI: 10.1038/s42003-022-03394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Invasive exotic pathogens pose a threat to trees and forest ecosystems worldwide, hampering the provision of essential ecosystem services such as carbon sequestration and water purification. Hybridization is a major evolutionary force that can drive the emergence of pathogens. Phytophthora ramorum, an emergent pathogen that causes the sudden oak and larch death, spreads as reproductively isolated divergent clonal lineages. We use a genomic biosurveillance approach by sequencing genomes of P. ramorum from survey and inspection samples and report the discovery of variants of P. ramorum that are the result of hybridization via sexual recombination between North American and European lineages. We show that these hybrids are viable, can infect a host and produce spores for long-term survival and propagation. Genome sequencing revealed genotypic combinations at 54,515 single nucleotide polymorphism loci not present in parental lineages. More than 6,000 of those genotypes are predicted to have a functional impact in genes associated with host infection, including effectors, carbohydrate-active enzymes and proteases. We also observed post-meiotic mitotic recombination that could generate additional genotypic and phenotypic variation and contribute to homoploid hybrid speciation. Our study highlights the importance of plant pathogen biosurveillance to detect variants, including hybrids, and inform management and control. Genome sequencing of isolates of the pathogen responsible for sudden oak death in the United States and sudden larch death in Europe reveal hybridisation between European and American lineages.
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Affiliation(s)
- Richard C Hamelin
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
| | | | - Renate Heinzelmann
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Kelly Hrywkiw
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Arnaud Capron
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Erika Dort
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Angela L Dale
- New Construction Materials, FPInnovations, Vancouver, BC, Canada
| | - Emilie Giroux
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Stacey Kus
- New Construction Materials, FPInnovations, Vancouver, BC, Canada
| | - Nick C Carleson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Horticultural Crops Research Unit, USDA ARS, Corvallis, OR, USA
| | - Nicolas Feau
- The Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
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18
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van Rees CB, Hand BK, Carter SC, Bargeron C, Cline TJ, Daniel W, Ferrante JA, Gaddis K, Hunter ME, Jarnevich CS, McGeoch MA, Morisette JT, Neilson ME, Roy HE, Rozance MA, Sepulveda A, Wallace RD, Whited D, Wilcox T, Kimball JS, Luikart G. A framework to integrate innovations in invasion science for proactive management. Biol Rev Camb Philos Soc 2022; 97:1712-1735. [PMID: 35451197 DOI: 10.1111/brv.12859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
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Affiliation(s)
- Charles B van Rees
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Sean C Carter
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Chuck Bargeron
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Timothy J Cline
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 2327 University Way STE 2, Bozeman MT 59717 & 320 Grinnel Drive, West Glacier, MT, 59936, U.S.A
| | - Wesley Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Keith Gaddis
- NASA Biological Diversity and Ecological Forecasting Programs, 300 E St. SW, Washington, DC, 20546, U.S.A
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Catherine S Jarnevich
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, U.S.A
| | - Melodie A McGeoch
- Department of Environment and Genetics, La Trobe University, Plenty Road & Kingsbury Drive, Bundoora, Victoria, 3086, Australia
| | - Jeffrey T Morisette
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB, U.K
| | - Mary Ann Rozance
- Northwest Climate Adaptation Science Center, University of Washington, Box 355674, Seattle, WA, 98195, U.S.A
| | - Adam Sepulveda
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Rebekah D Wallace
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Diane Whited
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Taylor Wilcox
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - John S Kimball
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Gordon Luikart
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
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19
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Santini A, Migliorini D. Invasive Alien Plant Pathogens: The Need of New Detection Methods. Methods Mol Biol 2022; 2536:111-118. [PMID: 35819601 DOI: 10.1007/978-1-0716-2517-0_7] [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] [Indexed: 06/15/2023]
Abstract
Invasive alien species are a major threat to natural and anthropogenic ecosystems and to the economy. Many invasive fungal species have severely impacted ecology and human lifestyle in the past. Most of them express a pathogenic lifestyle following introduction into a new region and hosts. They are usually cryptic during the introduction phase and hard to be identified, classified, and monitored.The increasing number of new alien pests coincide with the rapid increase in the volume and diversity of intercontinental trade in plants for planting, underlying the need to reduce the risk of their introduction with the development of molecular-based, inexpensive, rapid, accurate, and reliable methods that can identify and intercept plant pathogens even before symptoms occur in the new environment of diffusion. Applicative aerobiology, for instance, represents a challenging research line for the implementation of pest detection protocols during the early stage of fungal introduction, being capable to target aerial dispersed propagules.In addition to this, new metabarcoding protocols based on an innovative multigene approach, although not yet tested on fungi, are able to provide an output with very high taxonomic resolution and are likely to be considered in the next-future biosurveillance of invasive fungal pathogens.
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Affiliation(s)
- Alberto Santini
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Sesto Fiorentino, Florence, Italy
| | - Duccio Migliorini
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Sesto Fiorentino, Florence, Italy.
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20
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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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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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Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
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23
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Disentangling the genetic origin of Heracleum persicum (Apiaceae) in Europe: multiple introductions from multiple source populations. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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North HL, McGaughran A, Jiggins CD. Insights into invasive species from whole-genome resequencing. Mol Ecol 2021; 30:6289-6308. [PMID: 34041794 DOI: 10.1111/mec.15999] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.
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Affiliation(s)
- Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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VilÀ M, Dunn AM, Essl F, GÓmez-DÍaz E, Hulme PE, Jeschke JM, NÚÑez MA, Ostfeld RS, Pauchard A, Ricciardi A, Gallardo B. Viewing Emerging Human Infectious Epidemics through the Lens of Invasion Biology. Bioscience 2021. [DOI: 10.1093/biosci/biab047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Invasion biology examines species originated elsewhere and moved with the help of humans, and those species’ impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.
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Affiliation(s)
- Montserrat VilÀ
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | | | - Franz Essl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Elena GÓmez-DÍaz
- Institute of Parasitology and Biomedicine Lopez-Neyra, Granada, Spain
| | - Philip E Hulme
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand
| | - Jonathan M Jeschke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, with the Institute of Biology, Freie Universität Berlin, and with the Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - MartÍn A NÚÑez
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
| | - Richard S Ostfeld
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States
| | - AnÍbal Pauchard
- Laboratorio de Invasiones Biológicas, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile, and with the Institute of Ecology and Biodiversity, Santiago, Chile
| | | | - Belinda Gallardo
- Pyrenean Institute of Ecology, Zaragoza, Spain, and with the BioRISC (Biosecurity Research Initiative at St Catharine's), at St Catharine's College, Cambridge, United Kingdom
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Sparks ME, Hebert FO, Johnston JS, Hamelin R, Cusson M, Levesque R, Gundersen-Rindal DE. Sequencing, Assembly and Annotation of the Whole-Insect Genome of Lymantria dispar dispar, the European Gypsy Moth. G3-GENES GENOMES GENETICS 2021; 11:6261075. [PMID: 33930134 DOI: 10.1093/g3journal/jkab150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 11/14/2022]
Abstract
The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and GC content of 38.8%. Long interspersed nuclear elements (LINEs) constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.
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Affiliation(s)
- Michael E Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland 20705, USA
| | - Francois Olivier Hebert
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas 77843, USA
| | - Richard Hamelin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6.,Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Michel Cusson
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6.,Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Quebec City, Quebec, Canada, G1V 4C7
| | - Roger Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada, G1V 0A6
| | - Dawn E Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland 20705, USA
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Layne E, Dort EN, Hamelin R, Li Y, Blanchette M. Supervised learning on phylogenetically distributed data. Bioinformatics 2021; 36:i895-i902. [PMID: 33381838 DOI: 10.1093/bioinformatics/btaa842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The ability to develop robust machine-learning (ML) models is considered imperative to the adoption of ML techniques in biology and medicine fields. This challenge is particularly acute when data available for training is not independent and identically distributed (iid), in which case trained models are vulnerable to out-of-distribution generalization problems. Of particular interest are problems where data correspond to observations made on phylogenetically related samples (e.g. antibiotic resistance data). RESULTS We introduce DendroNet, a new approach to train neural networks in the context of evolutionary data. DendroNet explicitly accounts for the relatedness of the training/testing data, while allowing the model to evolve along the branches of the phylogenetic tree, hence accommodating potential changes in the rules that relate genotypes to phenotypes. Using simulated data, we demonstrate that DendroNet produces models that can be significantly better than non-phylogenetically aware approaches. DendroNet also outperforms other approaches at two biological tasks of significant practical importance: antiobiotic resistance prediction in bacteria and trophic level prediction in fungi. AVAILABILITY AND IMPLEMENTATION https://github.com/BlanchetteLab/DendroNet.
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Affiliation(s)
- Elliot Layne
- School of Computer Science, McGill, Montreal, QC H3A 0E9, Canada
| | - Erika N Dort
- Department of Forestry and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Richard Hamelin
- Department of Forestry and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yue Li
- School of Computer Science, McGill, Montreal, QC H3A 0E9, Canada
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Resh CA, Galaska MP, Benesh KC, Gardner JPA, Wei KJ, Yan RJ, Mahon AR. Using Genomics to Link Populations of an Invasive Species to Its Potential Sources. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.575599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The introduction and subsequent range expansion of the Northern snakehead (Channa argus: Channidae, Anabantiformes) is one of a growing number of problematic biological invasions in the United States. This harmful aquatic invasive species is a predatory freshwater fish native to northeastern Asia that, following deliberate introduction, has established itself in multiple water basins in the eastern United States, as well as expanding its range into the Midwest. Previous work assessed the population structure and estimated the long-term effective population sizes of the populations present in the United States, but the source of the initial introduction(s) to the U.S. remains unidentified. Building on earlier work, we used whole genome scans (2b-RAD genomic sequencing) to analyze single nucleotide polymorphisms (SNPs) from C. argus to screen the genomes of these invasive fish from United States waters and from three sites in their native range in China. We recovered 2,822 SNP loci from genomic DNA extracted from 164 fish sampled from the eastern United States and Arkansas (Mississippi River basin), plus 30 fish sampled from three regions of the Yangtze River basin in China (n = 10 individuals per basin). Our results provide evidence supporting the Yangtze River basin in China, specifically the Bohu and/or Liangzi lakes, is a likely source of the C. argus introductions in multiple regions of the U.S., including the Lower Hudson River basin, Upper Hudson River basin and Philadelphia (Lower Delaware River basin). This information, in conjunction with additional sampling from the native range, will help to determine the source(s) of introduction for the other U.S. populations. Additionally, this work will provide valuable information for management to help prevent and manage future introductions into United States waterways, as well as aid in the development of more targeted strategies to regulate established populations and inhibit further spread.
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Potential Differences and Methods of Determining Gypsy Moth Female Flight Capabilities: Implications for the Establishment and Spread in Novel Habitats. FORESTS 2021. [DOI: 10.3390/f12010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The introduction of the Asian gypsy moth into novel environments continues with frequent interceptions in North America. There is a concern that these subspecies will pose a greater threat to the forests and urban environments of North America than the established gypsy moths (Lymantria dispardispar L.), due to their greater capacity for female flight. Asian gypsy moth populations vary in many key traits, including female flight capabilities. The potential impacts of female flight, in combination with the other key traits, on the ecology and spread of this insect are first discussed in this communication. This also provides the first review of most of the current literature on the variations in flight capability and flight distance of gypsy moth populations, as well as variation in other traits of concern and the potential methods of identification, with special attention paid to the Asian subspecies Lymantria dispar japonica Motschulsky and Lymantria dispar asiatica Vinkovskij. There are currently good tools for identifying the general origin of introduced gypsy moth populations, but these do not provide enough information to effectively manage introductions. Gypsy moth key traits differ among populations, even within each subspecies of the gypsy moth, so introduction of gypsy moths from other world areas into locations where the gypsy moth is already present could result in unwanted changes in gypsy moth biology. It also appears that the introduction of flight-capable females could enhance a population’s dispersal capability and require modifications to management protocols used for flightless females. Therefore, rapid tools to assess key traits in introduced populations are needed to adequately plan for, or deal with, new introductions into novel habitats.
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30
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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Srivastava V, Roe AD, Keena MA, Hamelin RC, Griess VC. Oh the places they’ll go: improving species distribution modelling for invasive forest pests in an uncertain world. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02372-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paap T, Wingfield MJ, Burgess TI, Hulbert JM, Santini A. Harmonising the fields of invasion science and forest pathology. NEOBIOTA 2020. [DOI: 10.3897/neobiota.62.52991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Invasive alien species are widely recognised as significant drivers of global environmental change, with far reaching ecological and socio-economic impacts. The trend of continuous increases in first records, with no apparent sign of saturation, is consistent across all taxonomic groups. However, taxonomic biases exist in the extent to which invasion processes have been studied. Invasive forest pathogens have caused, and they continue to result in dramatic damage to natural forests and woody ecosystems, yet their impacts are substantially underrepresented in the invasion science literature. Conversely, most studies of forest pathogens have been undertaken in the absence of a connection to the frameworks developed and used to study biological invasions. We believe this is, in part, a consequence of the mechanistic approach of the discipline of forest pathology; one that has been inherited from the broader discipline of plant pathology. Rather than investigating the origins of, and the processes driving the arrival of invasive microorganisms, the focus of pathologists is generally to investigate specific interactions between hosts and pathogens, with an emphasis on controlling the resulting disease problems. In contrast, central to the field of invasion science, which finds its roots in ecology, is the development and testing of general concepts and frameworks. The lack of knowledge of microbial biodiversity and ecology, speciation and geographic origin present challenges in understanding invasive forest pathogens under existing frameworks, and there is a need to address this shortfall. Advances in molecular technologies such as gene and genome sequencing and metagenomics studies have increased the “visibility” of microorganisms. We consider whether these technologies are being adequately applied to address the gaps between forest pathology and invasion science. We also interrogate the extent to which the two fields stand to gain by becoming more closely linked.
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Brundu G, Pauchard A, Pyšek P, Pergl J, Bindewald AM, Brunori A, Canavan S, Campagnaro T, Celesti-Grapow L, Dechoum MDS, Dufour-Dror JM, Essl F, Flory SL, Genovesi P, Guarino F, Guangzhe L, Hulme PE, Jäger H, Kettle CJ, Krumm F, Langdon B, Lapin K, Lozano V, Le Roux JJ, Novoa A, Nuñez MA, Porté AJ, Silva JS, Schaffner U, Sitzia T, Tanner R, Tshidada N, Vítková M, Westergren M, Wilson JRU, Richardson DM. Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts. NEOBIOTA 2020. [DOI: 10.3897/neobiota.61.58380] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sustainably managed non-native trees deliver economic and societal benefits with limited risk of spread to adjoining areas. However, some plantations have launched invasions that cause substantial damage to biodiversity and ecosystem services, while others pose substantial threats of causing such impacts. The challenge is to maximise the benefits of non-native trees, while minimising negative impacts and preserving future benefits and options.
A workshop was held in 2019 to develop global guidelines for the sustainable use of non-native trees, using the Council of Europe – Bern Convention Code of Conduct on Invasive Alien Trees as a starting point.
The global guidelines consist of eight recommendations: 1) Use native trees, or non-invasive non-native trees, in preference to invasive non-native trees; 2) Be aware of and comply with international, national, and regional regulations concerning non-native trees; 3) Be aware of the risk of invasion and consider global change trends; 4) Design and adopt tailored practices for plantation site selection and silvicultural management; 5) Promote and implement early detection and rapid response programmes; 6) Design and adopt tailored practices for invasive non-native tree control, habitat restoration, and for dealing with highly modified ecosystems; 7) Engage with stakeholders on the risks posed by invasive non-native trees, the impacts caused, and the options for management; and 8) Develop and support global networks, collaborative research, and information sharing on native and non-native trees.
The global guidelines are a first step towards building global consensus on the precautions that should be taken when introducing and planting non-native trees. They are voluntary and are intended to complement statutory requirements under international and national legislation. The application of the global guidelines and the achievement of their goals will help to conserve forest biodiversity, ensure sustainable forestry, and contribute to the achievement of several Sustainable Development Goals of the United Nations linked with forest biodiversity.
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Assessing Niche Shifts and Conservatism by Comparing the Native and Post-Invasion Niches of Major Forest Invasive Species. INSECTS 2020; 11:insects11080479. [PMID: 32751077 PMCID: PMC7469212 DOI: 10.3390/insects11080479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 11/23/2022]
Abstract
Invasive species experience biotic and abiotic conditions that may (or may not) resemble their native environment. We explored the methodology of determining climatic niches and compared the native and post-invasion niches of four invasive forest pests to determine if these species experienced shifts or changes in their new climatic niches. We used environmental principle components analysis (PCA-env) method to quantify climatic niche shifts, expansions, and temporal changes. Furthermore, we assessed the effect of variable selection in the delineation and comparison of niche space. We found that variable selection influenced the delineation and overlap of each niche, whereas the subset of climatic variables selected from the first two PCA-env axes explained more variance in environmental conditions than the complete set of climatic variables for all four species. Most focal species showed climatic niche shifts in their invasive range and had not yet fully occupied the available niche within the invaded range. Our species varied the proportion of niche overlap between the native and invasive ranges. By comparing native and invasive niches, we can help predict a species’ potential range expansion and invasion potential. Our results can guide monitoring and help inform management of these and other invasive species.
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Schmidt TL, Chung J, Honnen AC, Weeks AR, Hoffmann AA. Population genomics of two invasive mosquitoes (Aedes aegypti and Aedes albopictus) from the Indo-Pacific. PLoS Negl Trop Dis 2020; 14:e0008463. [PMID: 32678817 PMCID: PMC7390453 DOI: 10.1371/journal.pntd.0008463] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/29/2020] [Accepted: 06/08/2020] [Indexed: 01/09/2023] Open
Abstract
The arbovirus vectors Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are both common throughout the Indo-Pacific region, where 70% of global dengue transmission occurs. For Ae. aegypti all Indo-Pacific populations are invasive, having spread from an initial native range of Africa, while for Ae. albopictus the Indo-Pacific includes invasive populations and those from the native range: putatively, India to Japan to Southeast Asia. This study analyses the population genomics of 480 of these mosquitoes sampled from 27 locations in the Indo-Pacific. We investigated patterns of genome-wide genetic differentiation to compare pathways of invasion and ongoing gene flow in both species, and to compare invasive and native-range populations of Ae. albopictus. We also tested landscape genomic hypotheses that genetic differentiation would increase with geographical distance and be lower between locations with high connectivity to human transportation routes, the primary means of dispersal at these scales. We found that genetic distances were generally higher in Ae. aegypti, with Pacific populations the most highly differentiated. The most differentiated Ae. albopictus populations were in Vanuatu, Indonesia and Sri Lanka, the latter two representing potential native-range populations and potential cryptic subspeciation respectively. Genetic distances in Ae. aegypti increased with geographical distance, while in Ae. albopictus they decreased with higher connectivity to human transportation routes. Contrary to the situation in Ae. aegypti, we found evidence of long-distance Ae. albopictus colonisation events, including colonisation of Mauritius from East Asia and of Fiji from Southeast Asia. These direct genomic comparisons indicate likely differences in dispersal ecology in these species, despite their broadly sympatric distributions and similar use of human transport to disperse. Our findings will assist biosecurity operations to trace the source of invasive material and for biocontrol operations that benefit from matching genetic backgrounds of released and local populations.
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Affiliation(s)
- Thomas L. Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica Chung
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
- Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia
| | - Ann-Christin Honnen
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrew R. Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
- cesar Pty Ltd, Parkville, Victoria, Australia
| | - Ary A. Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe. SUSTAINABILITY 2020. [DOI: 10.3390/su12114508] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.
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In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR. PLoS One 2020; 15:e0226863. [PMID: 32240194 PMCID: PMC7117680 DOI: 10.1371/journal.pone.0226863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/16/2020] [Indexed: 11/29/2022] Open
Abstract
Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.
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Isabel N, Holliday JA, Aitken SN. Forest genomics: Advancing climate adaptation, forest health, productivity, and conservation. Evol Appl 2020; 13:3-10. [PMID: 31892941 PMCID: PMC6935596 DOI: 10.1111/eva.12902] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
Forest ecosystems provide important ecological services and resources, from habitat for biodiversity to the production of environmentally friendly products, and play a key role in the global carbon cycle. Humanity is counting on forests to sequester and store a substantial portion of the anthropogenic carbon dioxide produced globally. However, the unprecedented rate of climate change, deforestation, and accidental importation of invasive insects and diseases are threatening the health and productivity of forests, and their capacity to provide these services. Knowledge of genetic diversity, local adaptation, and genetic control of key traits is required to predict the adaptive capacity of tree populations, inform forest management and conservation decisions, and improve breeding for productive trees that will withstand the challenges of the 21st century. Genomic approaches have well accelerated the generation of knowledge of the genetic and evolutionary underpinnings of nonmodel tree species, and advanced their applications to address these challenges. This special issue of Evolutionary Applications features 14 papers that demonstrate the value of a wide range of genomic approaches that can be used to better understand the biology of forest trees, including species that are widespread and managed for timber production, and others that are threatened or endangered, or serve important ecological roles. We highlight some of the major advances, ranging from understanding the evolution of genomes since the period when gymnosperms separated from angiosperms 300 million years ago to using genomic selection to accelerate breeding for tree health and productivity. We also discuss some of the challenges and future directions for applying genomic tools to address long-standing questions about forest trees.
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Affiliation(s)
- Nathalie Isabel
- Laurentian Forestry CentreCanadian Forest ServiceNatural Resources CanadaQuébecCanada
- Canada Research Chair in Forest GenomicsCentre for Forest Research and Institute for Systems and Integrative BiologyUniversité LavalQuébecCanada
| | - Jason A. Holliday
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVAUSA
| | - Sally N. Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverCanada
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Krehenwinkel H, Pomerantz A, Prost S. Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions. Genes (Basel) 2019; 10:E858. [PMID: 31671909 PMCID: PMC6895800 DOI: 10.3390/genes10110858] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology's MinION portable sequencing platform, as well as summarize areas of recent development.
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Affiliation(s)
| | - Aaron Pomerantz
- Department of Integrative Biology, University of California, Berkeley, CA-94720, USA.
- Marine Biology Laboratory, Woods Hole, MA-02543, USA.
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany.
- South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa.
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