1
|
Lodge DM. Conservation in a litre of air. Mol Ecol Resour 2024; 24:e13883. [PMID: 37864493 DOI: 10.1111/1755-0998.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
Since Ficetola et al. (2008) alerted ecologists and conservation biologists to the existence of environmental DNA (eDNA), the number of studies using eDNA has exploded, with a rapidly increasing diversity of research, monitoring, and management objectives. Initial applications focused on amphibians and fishes while today's taxonomic targets span the phylogenetic tree. The environmental media that are sampled have expanded from freshwater to saltwater to soils, and, most recently, to air. In this issue of Molecular Ecology Resources, Lynggaard et al. (Molecular Ecology Resources, 2023) use eDNA captured on air filters to census vertebrate biodiversity in a forest. With a three day, six sample period, 143 sample effort in a nature park in a rural area of Zealand, Denmark, their wild species detections comprised about 25% of the terrestrial vertebrates that are known to occur in the area, including about 33% of the mammal, 17% of the bird, and 60% of the amphibian species. This study demonstrates that air sampling for eDNA has the potential to become a powerful standard method for terrestrial biodiversity assessment that is complementary to traditional methods (e.g., trapping, visual and acoustic observation, collection of scat and hair).
Collapse
Affiliation(s)
- David M Lodge
- Cornell Atkinson Center for Sustainability, and the Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
2
|
Andrés J, Czechowski P, Grey E, Saebi M, Andres K, Brown C, Chawla N, Corbett JJ, Brys R, Cassey P, Correa N, Deveney MR, Egan SP, Fisher JP, Vanden Hooff R, Knapp CR, Leong SCY, Neilson BJ, Paolucci EM, Pfrender ME, Pochardt MR, Prowse TAA, Rumrill SS, Scianni C, Sylvester F, Tamburri MN, Therriault TW, Yeo DCJ, Lodge DM. Environment and shipping drive environmental DNA beta-diversity among commercial ports. Mol Ecol 2023; 32:6696-6709. [PMID: 36799015 DOI: 10.1111/mec.16888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship-borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping-stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship-borne species transport risks, particularly if the ports had similar environments and stepping-stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic-based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large-scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach.
Collapse
Affiliation(s)
- Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York, USA
| | - Paul Czechowski
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Helmholtz Institute for Metabolic, Obesity and Vascular Research, Leipzig, Germany
| | - Erin Grey
- School of Biology and Ecology and Maine Center for Genetics in the Environment, University of Maine, Orono, Maine, USA
- Division of Science, Mathematics and Technology, Governors State University, University Park, Illinois, USA
| | - Mandana Saebi
- Center for Network and Data Science (CNDS), University of Notre Dame, Notre Dame, Indiana, USA
| | - Kara Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York, USA
| | - Christopher Brown
- Golden Bear Research Center, California State University Maritime Academy, Vallejo, California, USA
| | - Nitesh Chawla
- Center for Network and Data Science (CNDS), University of Notre Dame, Notre Dame, Indiana, USA
| | - James J Corbett
- College of Earth, Ocean, and Environment, University of Delaware, Newark, Delaware, USA
| | - Rein Brys
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Phillip Cassey
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nancy Correa
- Servicio de Hidrografía Naval (Ministerio de Defensa), Buenos Aires, Argentina
- Escuela de Ciencias del Mar, Sede Educativa Universitaria, Facultad de la Armada, UNDEF, Buenos Aires, Argentina
| | - Marty R Deveney
- SARDI Aquatic Science and Marine Innovation SA, South Australian Research and Development Institute, West Beach, South Australia, Australia
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Joshua P Fisher
- United States Fish and Wildlife Service, Pacific Islands Fish and Wildlife Office, Honolulu, Hawaii, USA
| | | | - Charles R Knapp
- Daniel P. Haerther Center for Conservation and Research, Chicago, Illinois, USA
| | - Sandric Chee Yew Leong
- St. John's Island National Marine Laboratory, Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Brian J Neilson
- State of Hawaii Division of Aquatic Resources, Honolulu, Hawaii, USA
| | - Esteban M Paolucci
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Buenos Aires, Argentina
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana, USA
| | | | - Thomas A A Prowse
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Steven S Rumrill
- Marine Resources Program, Oregon Department of Fish and Wildlife, Newport, Oregon, USA
| | - Chris Scianni
- California State Lands Commission, Marine Invasive Species Program, Long Beach, California, USA
- Instituto para el Estudio de la Biodiversidad de Invertebrados, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Francisco Sylvester
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Mario N Tamburri
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, Maryland, USA
| | - Thomas W Therriault
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Darren C J Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - David M Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York, USA
| |
Collapse
|
3
|
Andres KJ, Lodge DM, Andrés J. Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes. Proc Natl Acad Sci U S A 2023; 120:e2307345120. [PMID: 37669387 PMCID: PMC10500163 DOI: 10.1073/pnas.2307345120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA approaches also hold great potential to obtain population-level genetic information from water samples. In this study, we sequenced a panel of multiallelic microsatellite markers from filtered water and fish tissue samples to uncover patterns of intraspecific diversity in the freshwater Round Goby (Neogobius melanostomus) across their invaded range in the Laurentian Great Lakes region. Although we found that the concentration of nuclear eDNA is lower than mitochondrial eDNA, we nonetheless detected over two-thirds of all nuclear alleles identified from genotyped tissues in our eDNA samples, with the greatest recovery of common alleles in the population. Estimates of allele frequencies and genetic variability within and between populations were detected from eDNA in patterns that were consistent with individual tissue-based estimates of genetic diversity and differentiation. The strongest genetic differentiation in both eDNA and tissues exists in an isolation by distance pattern. Our study demonstrates the potential for eDNA-based approaches to characterize key population parameters required to effectively monitor, manage, or sustain aquatic species.
Collapse
Affiliation(s)
- Kara J. Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
- Department of Biology, Washington University in St. Louis, St. Louis, MO63130
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO63130
| | - David M. Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY14853
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY14853
| |
Collapse
|
4
|
Andres KJ, Lodge DM, Sethi SA, Andrés J. Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance. Mol Ecol 2023. [PMID: 37254233 DOI: 10.1111/mec.17031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/21/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections in diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies have explored the potential for these approaches to detect within-species genetic variation, allowing for population genetic assessments and abundance estimates from environmental samples. However, we currently lack a framework outlining the key considerations specific to generating, analysing and applying eDNA data for these two purposes. Here, we discuss how various genetic markers differ with regard to genetic information and detectability in environmental samples and how analysis of eDNA samples differs from common tissue-based analyses. We then outline how it may be possible to obtain species absolute abundance estimates from eDNA by detecting intraspecific genetic variation in mixtures of DNA under multiple scenarios. We also identify the major causes contributing to allele detection and frequency errors in eDNA data, discuss their consequences for population-level analyses and outline bioinformatic approaches to detect and remove erroneous sequences. This review summarizes the key advances required to harness the full potential of eDNA-based intraspecific genetic variation to inform population-level questions in ecology, evolutionary biology and conservation management.
Collapse
Affiliation(s)
- Kara J Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - David M Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York, USA
| | - Suresh A Sethi
- Fisheries, Aquatic Science and Technology Laboratory, Alaska Pacific University, Anchorage, Alaska, USA
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
5
|
Szydlowski DK, Elgin AK, Lodge DM, Tiemann JS, Larson ER. Long-term macrophyte and snail community responses to population declines of invasive rusty crayfish (Faxonius rusticus). Ecol Appl 2023; 33:e2818. [PMID: 36772970 DOI: 10.1002/eap.2818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
A central focus of invasive species research has been on human efforts to eradicate invaders or reduce their abundance to mitigate the worst of their impacts. In some cases, however, populations of invasive species decline without human intervention, which may inform management responses to these invaders. Such is the case of the invasive rusty crayfish (Faxonius rusticus) in northern Wisconsin, USA, where systematic population monitoring since 1975 has revealed population declines in approximately half of the lakes surveyed. Population declines of invasive species without human intervention remain understudied, but there is even less research on how communities respond following such declines. Using 10 lakes in Vilas County, Wisconsin, we investigated community recovery of habitat (macrophytes) and prey (freshwater snails) of F. rusticus following up to 33 years of declines of this invader in some lakes using a dataset with a rare, long-term span over which consistent data were collected (1987, 2002, 2011, and 2020). We compared community responses in lakes where F. rusticus populations reached a peak and subsequently declined (boom-bust lakes) and lakes where our dataset only captured the decline of F. rusticus (bust lakes) to reference lakes with consistently high or low crayfish abundance over time. We found partial recovery of macrophytes and snails in the bust and boom-bust lakes where F. rusticus has declined, with recovery of macrophyte abundance and richness in the boom-bust lakes achieving levels observed in the low-crayfish reference lakes. Snail abundance and richness increased after declines of F. rusticus, though not to the level of the low-crayfish reference lakes, suggesting that snail recovery may lag macrophyte recovery because snails are dependent on macrophytes and associated periphyton for habitat. The recovery we document potentially represents long-term ecosystem resilience of lakes to biological invasions. Our results suggest that lake communities may recover without active restoration interventions after invasive crayfish population declines, although identifying which lakes experience these natural declines remains a priority for future research and management.
Collapse
Affiliation(s)
- Daniel K Szydlowski
- Department of Natural Resources and Environmental Sciences, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
| | - Ashley K Elgin
- National Oceanic and Atmospheric Administration, Great Lakes Environmental Research Laboratory, Muskegon, Michigan, USA
| | - David M Lodge
- Cornell Atkinson Center for Sustainability, and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jeremy S Tiemann
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
| | - Eric R Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
| |
Collapse
|
6
|
Halpern BS, Boettiger C, Dietze MC, Gephart JA, Gonzalez P, Grimm NB, Groffman PM, Gurevitch J, Hobbie SE, Komatsu KJ, Kroeker KJ, Lahr HJ, Lodge DM, Lortie CJ, Lowndes JSS, Micheli F, Possingham HP, Ruckelshaus MH, Scarborough C, Wood CL, Wu GC, Aoyama L, Arroyo EE, Bahlai CA, Beller EE, Blake RE, Bork KS, Branch TA, Brown NEM, Brun J, Bruna EM, Buckley LB, Burnett JL, Castorani MCN, Cheng SH, Cohen SC, Couture JL, Crowder LB, Dee LE, Dias AS, Diaz‐Maroto IJ, Downs MR, Dudney JC, Ellis EC, Emery KA, Eurich JG, Ferriss BE, Fredston A, Furukawa H, Gagné SA, Garlick SR, Garroway CJ, Gaynor KM, González AL, Grames EM, Guy‐Haim T, Hackett E, Hallett LM, Harms TK, Haulsee DE, Haynes KJ, Hazen EL, Jarvis RM, Jones K, Kandlikar GS, Kincaid DW, Knope ML, Koirala A, Kolasa J, Kominoski JS, Koricheva J, Lancaster LT, Lawlor JA, Lowman HE, Muller‐Karger FE, Norman KEA, Nourn N, O'Hara CC, Ou SX, Padilla‐Gamino JL, Pappalardo P, Peek RA, Pelletier D, Plont S, Ponisio LC, Portales‐Reyes C, Provete DB, Raes EJ, Ramirez‐Reyes C, Ramos I, Record S, Richardson AJ, Salguero‐Gómez R, Satterthwaite EV, Schmidt C, Schwartz AJ, See CR, Shea BD, Smith RS, Sokol ER, Solomon CT, Spanbauer T, Stefanoudis PV, Sterner BW, Sudbrack V, Tonkin JD, Townes AR, Valle M, Walter JA, Wheeler KI, Wieder WR, Williams DR, Winter M, Winterova B, Woodall LC, Wymore AS, Youngflesh C. Priorities for synthesis research in ecology and environmental science. Ecosphere 2023. [DOI: 10.1002/ecs2.4342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Benjamin S. Halpern
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
- Bren School of Environmental Science and Management University of California Santa Barbara California USA
| | - Carl Boettiger
- Department of Environmental Science, Policy, and Management University of California Berkeley California USA
| | - Michael C. Dietze
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - Jessica A. Gephart
- Department of Environmental Science American University Washington District of Columbia USA
| | - Patrick Gonzalez
- Department of Environmental Science, Policy, and Management University of California Berkeley California USA
- Institute for Parks, People, and Biodiversity University of California Berkeley California USA
| | - Nancy B. Grimm
- School of Life Sciences Arizona State University Tempe Arizona USA
| | - Peter M. Groffman
- City University of New York Advanced Science Research Center at the Graduate Center New York New York USA
- Cary Institute of Ecosystem Studies Millbrook New York USA
| | - Jessica Gurevitch
- Department of Ecology and Evolution Stony Brook University Stony Brook New York USA
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and Behavior University of Minnesota St. Paul Minnesota USA
| | | | - Kristy J. Kroeker
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California USA
| | - Heather J. Lahr
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - David M. Lodge
- Cornell Atkinson Center for Sustainability Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Christopher J. Lortie
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
- Department of Biology York University Toronto Ontario Canada
| | - Julie S. S. Lowndes
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Fiorenza Micheli
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
- Stanford Center for Ocean Solutions Pacific Grove California USA
| | - Hugh P. Possingham
- Centre for Biodiversity and Conservation Science (CBCS) The University of Queensland Brisbane Queensland Australia
| | | | - Courtney Scarborough
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Chelsea L. Wood
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Grace C. Wu
- Environmental Studies University of California Santa Barbara California USA
| | - Lina Aoyama
- Environmental Studies Program and Department of Biology University of Oregon Eugene Oregon USA
| | - Eva E. Arroyo
- Department of Ecology Evolution and Environmental Biology New York New York USA
| | | | - Erin E. Beller
- Real Estate and Workplace Services Sustainability Team Google Inc. Mountain View California USA
| | | | | | - Trevor A. Branch
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Norah E. M. Brown
- Department of Biology University of Victoria Victoria British Columbia Canada
| | - Julien Brun
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Emilio M. Bruna
- Department of Wildlife Ecology & Conservation University of Florida Gainesville Florida USA
| | - Lauren B. Buckley
- Department of Biology University of Washington Seattle Washington USA
| | - Jessica L. Burnett
- Core Science Systems Science Analytics and Synthesis U.S. Geological Survey, 8th and Kipling, Denver Federal Center Lakewood Colorado USA
| | - Max C. N. Castorani
- Department of Environmental Sciences University of Virginia Charlottesville Virginia USA
| | - Samantha H. Cheng
- Center for Biodiversity and Conservation American Museum of Natural History New York New York USA
| | - Sarah C. Cohen
- Estuary and Ocean Science Center, Biology Department San Francisco State University San Francisco California USA
| | | | - Larry B. Crowder
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
| | - Laura E. Dee
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Arildo S. Dias
- Department of Physical Geography (IPG) Goethe‐Universität Frankfurt (Campus Riedberg) Frankfurt am Main Germany
| | | | - Martha R. Downs
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Joan C. Dudney
- Department of Plant Sciences UC Davis Davis California USA
| | - Erle C. Ellis
- Geography & Environmental Systems University of Maryland Baltimore Maryland USA
| | - Kyle A. Emery
- Department of Geography UC Los Angeles Los Angeles California USA
| | | | - Bridget E. Ferriss
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA Seattle Washington USA
| | - Alexa Fredston
- Department of Ocean Sciences University of California Santa Cruz California USA
| | - Hikaru Furukawa
- School of Earth and Space Exploration Arizona State University Tempe Arizona USA
| | - Sara A. Gagné
- Department of Geography and Earth Sciences University of North Carolina at Charlotte Charlotte North Carolina USA
| | | | - Colin J. Garroway
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Kaitlyn M. Gaynor
- Departments of Zoology and Botany University of British Columbia Vancouver British Columbia Canada
| | - Angélica L. González
- Department of Biology & Center for Computational and Integrative Biology Rutgers University Camden New Jersey USA
| | - Eliza M. Grames
- Department of Biology University of Nevada, Reno Reno Nevada USA
| | - Tamar Guy‐Haim
- National Institute of Oceanography Israel Oceanographic and Limnological Research (IOLR) Haifa Israel
| | - Ed Hackett
- School of Human Evolution & Social Change Arizona State University Tempe Arizona USA
| | - Lauren M. Hallett
- Environmental Studies Program and Department of Biology University of Oregon Eugene Oregon USA
| | - Tamara K. Harms
- Institute of Arctic Biology and Department of Biology & Wildlife University of Alaska Fairbanks Fairbanks Alaska USA
| | - Danielle E. Haulsee
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
| | - Kyle J. Haynes
- Blandy Experimental Farm University of Virginia Boyce Virginia USA
| | - Elliott L. Hazen
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California USA
| | - Rebecca M. Jarvis
- School of Science Auckland University of Technology Auckland New Zealand
| | | | - Gaurav S. Kandlikar
- Division of Biological Sciences & Division of Plant Sciences University of Missouri Columbia Missouri USA
| | - Dustin W. Kincaid
- Vermont EPSCoR and Gund Institute for Environment University of Vermont Burlington Vermont USA
| | - Matthew L. Knope
- Department of Biology University of Hawai'i at Hilo Hilo Hawaii USA
| | - Anil Koirala
- Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia USA
| | - Jurek Kolasa
- Department of Biology McMaster University Hamilton Ontario Canada
| | - John S. Kominoski
- Institute of Environment Florida International University Miami Florida USA
| | - Julia Koricheva
- Department of Biological Sciences Royal Holloway University of London Surrey UK
| | | | - Jake A. Lawlor
- Department of Biology McGill University Montreal Quebec Canada
| | - Heili E. Lowman
- Department of Natural Resources and Environmental Science University of Nevada, Reno Reno Nevada USA
| | | | - Kari E. A. Norman
- Département de sciences biologiques Université de Montréal Montréal Québec Canada
| | - Nan Nourn
- Department of Fisheries and Wildlife Michigan State University East Lansing Michigan USA
| | - Casey C. O'Hara
- Bren School of Environmental Science and Management University of California Santa Barbara California USA
| | - Suzanne X. Ou
- Department of Biology Stanford University Stanford California USA
| | | | - Paula Pappalardo
- Marine Invasions Laboratory Smithsonian Environmental Research Center Tiburon California USA
| | - Ryan A. Peek
- Center for Watershed Sciences University of California Davis California USA
| | - Dominique Pelletier
- UMR DECOD, HALGO, Département Ressources Biologiques et Environnement Institut Français de Recherche pour l'Exploitation de la Mer Lorient France
| | - Stephen Plont
- Department of Biological Sciences Virginia Polytechnic Institute and State University Blacksburg Virginia USA
| | - Lauren C. Ponisio
- Institute of Ecology and Evolution, Department of Biology University of Oregon Eugene Oregon USA
| | | | - Diogo B. Provete
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
| | - Eric J. Raes
- Minderoo Foundation, Flourishing Oceans Nedlands Western Australia Australia
| | | | - Irene Ramos
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO) Mexico City Mexico
| | - Sydne Record
- Department of Wildlife, Fisheries, and Conservation Biology University of Maine Orono Maine USA
| | - Anthony J. Richardson
- School of Mathematics and Physics University of Queensland St Lucia Queensland Australia
| | | | - Erin V. Satterthwaite
- California Sea Grant Scripps Institution of Oceanography, University of California, San Diego La Jolla California USA
| | - Chloé Schmidt
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Aaron J. Schwartz
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Craig R. See
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona USA
| | - Brendan D. Shea
- Department of Fish and Wildlife Conservation Virginia Tech Blacksburg Virginia USA
| | - Rachel S. Smith
- Department of Environmental Sciences University of Virginia Charlottesville Virginia USA
| | - Eric R. Sokol
- Battelle, National Ecological Observatory Network (NEON) Boulder Colorado USA
| | | | - Trisha Spanbauer
- Department of Environmental Sciences/Lake Erie Center University of Toledo Toledo Ohio USA
| | | | | | - Vitor Sudbrack
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Jonathan D. Tonkin
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Ashley R. Townes
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Mireia Valle
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA) Sukarrieta Spain
| | - Jonathan A. Walter
- Center for Watershed Sciences University of California Davis California USA
| | - Kathryn I. Wheeler
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - William R. Wieder
- Climate and Global Dynamics Laboratory, Terrestrial Sciences Section National Center for Atmospheric Research Boulder Colorado USA
| | - David R. Williams
- Sustainability Research Institute, School of Earth and Environment University of Leeds Leeds UK
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Barbora Winterova
- Department of Botany and Zoology, Faculty of Science Masaryk University Brno Czech Republic
| | - Lucy C. Woodall
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Adam S. Wymore
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Casey Youngflesh
- Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
| |
Collapse
|
7
|
Newcomb TJ, Simonin PW, Martinez FA, Chadderton WL, Bossenbroek JM, Cudmore B, Hoff MH, Keller RP, Ridenhour BD, Rothlisberger JD, Rutherford ES, Van Egeren S, Lodge DM. A Best Practices Case Study for Scientific Collaboration between Researchers and Managers. Fisheries (Bethesda) 2021; 46:131-138. [PMID: 33888934 PMCID: PMC8048992 DOI: 10.1002/fsh.10536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/15/2020] [Accepted: 09/27/2020] [Indexed: 06/12/2023]
Abstract
Effective engagement among scientists, government agency staff, and policymakers is necessary for solving fisheries challenges, but remains challenging for a variety of reasons. We present seven practices learned from a collaborative project focused on invasive species in the Great Lakes region (USA-CAN). These practices were based on a researcher-manager model composed of a research team, a management advisory board, and a bridging organization. We suggest this type of system functions well when (1) the management advisory board is provided compelling rationale for engagement; (2) the process uses key individuals as communicators; (3) the research team thoughtfully selects organizations and individuals involved; (4) the funding entity provides logistical support and allows for (5) a flexible structure that prioritizes management needs; (6) a bridging organization sustains communication between in-person meetings; and (7) the project team determines and enacts a project endpoint. We predict these approaches apply equally effectively to other challenges at the research-management-policy interface, including reductions of water pollution, transitions to renewable energy, increasing food security, and addressing climate change.
Collapse
Affiliation(s)
| | - Paul W. Simonin
- Cornell UniversityDepartment of Ecology and Evolutionary BiologyIthacaNY
| | - Felix A. Martinez
- National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean ScienceAnn ArborMI
| | | | - Jon M. Bossenbroek
- Department of Environmental Sciences and Lake Erie CenterUniversity of ToledoToledoOH
| | | | - Michael H. Hoff
- U.S. Fish and Wildlife Service (retired), Fish and Aquatic ConservationBloomingtonMN
| | - Reuben P. Keller
- Loyola University ChicagoInstitute of Environmental SustainabilityChicagoIL
| | - Berkley D. Ridenhour
- The Nature Conservancy, Great Lakes ProjectSouth BendIN
- The Nature ConservancyMoscowID
| | | | - Edward S. Rutherford
- National Oceanic and Atmospheric AdministrationGreat Lakes Environmental Research LaboratoryAnn ArborMI
| | | | - David M. Lodge
- Cornell UniversityCornell Atkinson Center for SustainabilityIthacaNY
- University of Notre DameEnvironmental Change InitiativeSouth BendIN (former)
| |
Collapse
|
8
|
Andres KJ, Sethi SA, Lodge DM, Andrés J. Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples. Mol Ecol 2021; 30:685-697. [PMID: 33433059 PMCID: PMC7898893 DOI: 10.1111/mec.15765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022]
Abstract
Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA-based and individual tissue-based estimates of allele frequencies from experimental mesocosms and in a field-based trial. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. With this study we document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population-level genetic diversity.
Collapse
Affiliation(s)
- Kara J Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Suresh A Sethi
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Unit, Cornell University, Ithaca, NY, USA
| | - David M Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, USA
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
9
|
Saebi M, Xu J, Curasi SR, Grey EK, Chawla NV, Lodge DM. Network analysis of ballast-mediated species transfer reveals important introduction and dispersal patterns in the Arctic. Sci Rep 2020; 10:19558. [PMID: 33177658 PMCID: PMC7658980 DOI: 10.1038/s41598-020-76602-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/22/2020] [Indexed: 11/09/2022] Open
Abstract
Rapid climate change has wide-ranging implications for the Arctic region, including sea ice loss, increased geopolitical attention, and expanding economic activity resulting in a dramatic increase in shipping activity. As a result, the risk of harmful non-native marine species being introduced into this critical region will increase unless policy and management steps are implemented in response. Using data about shipping, ecoregions, and environmental conditions, we leverage network analysis and data mining techniques to assess, visualize, and project ballast water-mediated species introductions into the Arctic and dispersal of non-native species within the Arctic. We first identify high-risk connections between the Arctic and non-Arctic ports that could be sources of non-native species over 15 years (1997-2012) and observe the emergence of shipping hubs in the Arctic where the cumulative risk of non-native species introduction is increasing. We then consider how environmental conditions can constrain this Arctic introduction network for species with different physiological limits, thus providing a tool that will allow decision-makers to evaluate the relative risk of different shipping routes. Next, we focus on within-Arctic ballast-mediated species dispersal where we use higher-order network analysis to identify critical shipping routes that may facilitate species dispersal within the Arctic. The risk assessment and projection framework we propose could inform risk-based assessment and management of ship-borne invasive species in the Arctic.
Collapse
Affiliation(s)
- Mandana Saebi
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Network and Data Science (CNDS), Notre Dame, IN, 46556, USA
| | - Jian Xu
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
- Citadel LLC, Chicago, IL, 60603, USA
| | - Salvatore R Curasi
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Erin K Grey
- Division of Science, Mathematics and Technology, Governors State University, University Park, IL, 60484, USA
| | - Nitesh V Chawla
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Network and Data Science (CNDS), Notre Dame, IN, 46556, USA
| | - David M Lodge
- Cornell Atkinson Center for Sustainability, and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA.
| |
Collapse
|
10
|
McElroy ME, Dressler TL, Titcomb GC, Wilson EA, Deiner K, Dudley TL, Eliason EJ, Evans NT, Gaines SD, Lafferty KD, Lamberti GA, Li Y, Lodge DM, Love MS, Mahon AR, Pfrender ME, Renshaw MA, Selkoe KA, Jerde CL. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
11
|
Larson ER, Kreps TA, Peters B, Peters JA, Lodge DM. Habitat explains patterns of population decline for an invasive crayfish. Ecology 2019; 100:e02659. [PMID: 30919952 DOI: 10.1002/ecy.2659] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 11/11/2022]
Abstract
Invasive nonindigenous species are defined by their impacts: they substantially change native communities or ecosystems. Accordingly, invasive species might transform their habitats in ways that eventually become unfavorable to them, causing population declines or even extirpations. Here we use over 40 yr of systematically collected data on the abundance of the invasive rusty crayfish Faxonius rusticus from 17 lakes in northern Wisconsin, USA to explore whether population declines of this invader are related to the prevalence of rocky habitat, which shelters crayfish from predators and is unchanged by crayfish. We predicted that lakes with rock-dominated substrates would be resistant to F. rusticus population declines, whereas lakes lacking rock-dominated substrates would experience F. rusticus declines due to crayfish destruction of shelter-providing macrophytes. We found that in nearly one-half (47%) of the study lakes, F. rusticus experienced population declines over the study time period, and these lakes had significantly lower proportions of rock substrate than lakes that did not experience population declines. We recommend that more studies should investigate the potential for invasive species-mediated community or ecosystem feedbacks to eventually contribute to their own population declines.
Collapse
Affiliation(s)
- Eric R Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, 61801, USA
| | - Timothy A Kreps
- Department of Biology, Bridgewater College, Bridgewater, Virginia, 22812, USA
| | - Brett Peters
- Environmental Change Initiative, University of Notre Dame, South Bend, Indiana, 46617, USA
| | - Jody A Peters
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556, USA
| | - David M Lodge
- Environmental Change Initiative, University of Notre Dame, South Bend, Indiana, 46617, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556, USA.,Atkinson Center for a Sustainable Future, Cornell University, Ithaca, New York, 14853, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| |
Collapse
|
12
|
Deiner K, Lopez J, Bourne S, Holman L, Seymour M, Grey EK, Lacoursière A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. MBMG 2018. [DOI: 10.3897/mbmg.2.28963] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 µm, 0.7 µm and 1.2 µm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styelaclava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples.
Collapse
|
13
|
Lacoursière‐Roussel A, Howland K, Normandeau E, Grey EK, Archambault P, Deiner K, Lodge DM, Hernandez C, Leduc N, Bernatchez L. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol 2018; 8:7763-7777. [PMID: 30250661 PMCID: PMC6144963 DOI: 10.1002/ece3.4213] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.
Collapse
Affiliation(s)
| | - Kimberly Howland
- Central and Arctic RegionFisheries and Oceans CanadaFreshwater InstituteWinnipegMBCanada
| | - Eric Normandeau
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Erin K. Grey
- Division of Science, Mathematics and TechnologyGovernors State UniversityUniversity ParkILUSA
| | | | - Kristy Deiner
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - David M. Lodge
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Cecilia Hernandez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Noémie Leduc
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Louis Bernatchez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| |
Collapse
|
14
|
Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Deiner K, Lodge DM, Lamberti GA, Pfrender ME. Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding. MBMG 2018. [DOI: 10.3897/mbmg.2.24262] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transport than in high-discharge streams. We estimated α- and β-diversity of the fish community from eDNA samples collected in a small Michigan (USA) stream from its headwaters to its confluence with a larger river. We found that α-diversity increased from upstream to downstream and, as predicted, we found a significant positive correlation between β-diversity and physical distance (stream length) between locations indicating species turnover along the longitudinal stream gradient. Sample replicates and different genetic markers showed similar species composition, supporting the consistency of the eDNA metabarcoding approach to estimate α- and β-diversity of fishes in low-discharge streams.
Collapse
|
15
|
Vincelli P, Jackson-Smith D, Holsapple M, Grusak MA, Harsh M, Klein T, Lambert J, Lange BM, Lodge DM, McCluskey J, Murphy A, Neuhouser ML, Pray C, Weller S. National Academies report has broad support. Nat Biotechnol 2018; 35:304-306. [PMID: 28398324 DOI: 10.1038/nbt.3842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul Vincelli
- Sustainable Agriculture Research and Education Program (SARE) and the University of Kentucky, Lexington, Kentucky, USA
| | - Douglas Jackson-Smith
- Rural Sociological Society and School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, USA
| | - Michael Holsapple
- Society of Toxicology, Center for Research on Ingredient Safety (CRIS) and Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Michael A Grusak
- Crop Science Society of America, USDA-ARS Children's Nutrition Research Center and Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Matthew Harsh
- Society for Social Studies of Science and Centre for Engineering in Society, Concordia University, Montreal, Quebec, Canada
| | - Theodore Klein
- Society for In Vitro Biology and Meristematic, Inc., San Francisco, California, USA
| | - James Lambert
- Society for Risk Analysis and University of Virginia, Charlottesville, Virginia, USA
| | - B Markus Lange
- Phytochemical Society of North America and Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - David M Lodge
- Ecological Society of America and Atkinson Center for a Sustainable Future, Cornell University, Ithaca, New York, USA
| | - Jill McCluskey
- School of Economic Sciences, Washington State University, Pullman, Washington, USA
| | - Angus Murphy
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Marian L Neuhouser
- American Society for Nutrition and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carl Pray
- International Consortium for Applied Bioeconomy Research and Department of Agriculture, Food, and Resource Economics, Rutgers University, New Brunswick, New Jersey, USA
| | - Susan Weller
- Entomological Society of America and University of Nebraska State Museum, Lincoln, Nebraska, USA
| |
Collapse
|
16
|
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol 2017; 26:5872-5895. [PMID: 28921802 DOI: 10.1111/mec.14350] [Citation(s) in RCA: 583] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
Collapse
Affiliation(s)
- Kristy Deiner
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Holly M Bik
- Department of Nematology, University of California, Riverside, CA, USA
| | - Elvira Mächler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | | | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK
| | - Iliana Bista
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales Building, Bangor University, Bangor, Gwynedd, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David M Lodge
- Atkinson Center for a Sustainable Future, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Natasha de Vere
- Conservation and Research Department, National Botanic Garden of Wales, Llanarthne, Carmarthenshire, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
| |
Collapse
|
17
|
Kramer AM, Annis G, Wittmann ME, Chadderton WL, Rutherford ES, Lodge DM, Mason L, Beletsky D, Riseng C, Drake JM. Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat. Ecosphere 2017. [DOI: 10.1002/ecs2.1883] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Andrew M. Kramer
- Odum School of Ecology; University of Georgia; Athens Georgia 30602 USA
| | - Gust Annis
- The Nature Conservancy; Lansing Michigan 48906 USA
| | - Marion E. Wittmann
- Department of Biological Sciences; University of Notre Dame; Notre Dame Indiana 46556 USA
- Natural Reserve System; University of California; Santa Barbara California 93106 USA
| | | | - Edward S. Rutherford
- NOAA Great Lakes Environmental Research Laboratory; Ann Arbor Michigan 48108 USA
| | - David M. Lodge
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York 14853 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame Indiana 46556 USA
| | - Lacey Mason
- School of Natural Resources and Environment; University of Michigan; Ann Arbor Michigan 48109 USA
| | - Dmitry Beletsky
- School for Environment and Sustainability; Cooperative Institute for Great Lakes Research; University of Michigan; Ann Arbor Michigan 48108 USA
| | - Catherine Riseng
- School of Natural Resources and Environment; University of Michigan; Ann Arbor Michigan 48109 USA
| | - John M. Drake
- Odum School of Ecology; University of Georgia; Athens Georgia 30602 USA
| |
Collapse
|
18
|
Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME. Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12836] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristy Deiner
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Mark A. Renshaw
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Yiyuan Li
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Brett P. Olds
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - David M. Lodge
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| | - Michael E. Pfrender
- Department of Biological Sciences Environmental Change Initiative University of Notre Dame Notre Dame IN USA
| |
Collapse
|
19
|
Affiliation(s)
- Lindsey S. Reisinger
- Department of Biological Sciences; University of Notre Dame; Notre Dame Indiana 46556 USA
| | - David M. Lodge
- Environmental Change Initiative and Department of Biological Sciences; University of Notre Dame; Notre Dame Indiana 46556 USA
| |
Collapse
|
20
|
Olds BP, Jerde CL, Renshaw MA, Li Y, Evans NT, Turner CR, Deiner K, Mahon AR, Brueseke MA, Shirey PD, Pfrender ME, Lodge DM, Lamberti GA. Estimating species richness using environmental DNA. Ecol Evol 2016; 6:4214-26. [PMID: 27516876 PMCID: PMC4972244 DOI: 10.1002/ece3.2186] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/03/2022] Open
Abstract
The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion‐based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.
Collapse
Affiliation(s)
- Brett P Olds
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana; Shrimp Department Oceanic Institute at Hawai'i Pacific University Waimanalo Hawaii
| | - Christopher L Jerde
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana; Biology Department University of Nevada Reno Nevada
| | - Mark A Renshaw
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Yiyuan Li
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Nathan T Evans
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Cameron R Turner
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Kristy Deiner
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Andrew R Mahon
- Department of Biology Institute for Great Lakes Research Central Michigan University Mount Pleasant Michigan
| | - Michael A Brueseke
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Patrick D Shirey
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Michael E Pfrender
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - David M Lodge
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| | - Gary A Lamberti
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana
| |
Collapse
|
21
|
Bobeldyk AM, Bossenbroek JM, Evans-White MA, Lodge DM, Lamberti GA. Secondary spread of zebra mussels (Dreissena polymorpha) in coupled lake-stream systems. Écoscience 2016. [DOI: 10.2980/i1195-6860-12-3-339.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
22
|
Dougherty MM, Larson ER, Renshaw MA, Gantz CA, Egan SP, Erickson DM, Lodge DM. Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances. J Appl Ecol 2016; 53:722-732. [PMID: 27773942 PMCID: PMC5053277 DOI: 10.1111/1365-2664.12621] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/02/2016] [Indexed: 11/27/2022]
Abstract
Early detection is invaluable for the cost‐effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates and also tested the relationship between eDNA copy number and O. rusticus relative abundance. We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods.
Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods.
Collapse
Affiliation(s)
- Matthew M Dougherty
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA; Catholic Theological Union Chicago IL 60615 USA
| | - Eric R Larson
- Daniel P. Haerther Center for Conservation and Research John G. Shedd Aquarium Chicago IL 60605 USA; Environmental Change Initiative University of Notre Dame South Bend IN 46617 USA; Department of Natural Resources and Environmental Sciences University of Illinois Urbana IL 61801 USA
| | - Mark A Renshaw
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Crysta A Gantz
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Scott P Egan
- Department of BioSciences Rice University Houston TX 77251 USA
| | - Daniel M Erickson
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - David M Lodge
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA; Environmental Change Initiative University of Notre Dame South Bend IN 46617 USA
| |
Collapse
|
23
|
Wittmann ME, Barnes MA, Jerde CL, Jones LA, Lodge DM. Confronting species distribution model predictions with species functional traits. Ecol Evol 2016; 6:873-9. [PMID: 26941933 PMCID: PMC4761765 DOI: 10.1002/ece3.1898] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/22/2015] [Accepted: 11/25/2015] [Indexed: 12/02/2022] Open
Abstract
Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.
Collapse
Affiliation(s)
- Marion E. Wittmann
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana46556
- Department of BiologyUniversity of Nevada RenoRenoNevada89509
| | - Matthew A. Barnes
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana46556
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana46556
- Department of Natural Resources ManagementTexas Tech UniversityLubbockTexas79409
| | - Christopher L. Jerde
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana46556
- Department of BiologyUniversity of Nevada RenoRenoNevada89509
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana46556
| | - Lisa A. Jones
- Fisheries and Oceans CanadaGreat Lakes Laboratory for Fisheries and Aquatic SciencesBurlingtonON L7S 1A1Canada
| | - David M. Lodge
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana46556
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana46556
| |
Collapse
|
24
|
Howeth JG, Gantz CA, Angermeier PL, Frimpong EA, Hoff MH, Keller RP, Mandrak NE, Marchetti MP, Olden JD, Romagosa CM, Lodge DM. Predicting invasiveness of species in trade: climate match, trophic guild and fecundity influence establishment and impact of non-native freshwater fishes. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12391] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jennifer G. Howeth
- Department of Biological Sciences; University of Alabama; Tuscaloosa AL 35487 USA
| | - Crysta A. Gantz
- Department of Biological Sciences and Notre Dame Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| | - Paul L. Angermeier
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; Blacksburg VA 24061 USA
- U. S. Geological Survey; Virginia Cooperative Fish and Wildlife Research Unit; Virginia Polytechnic Institute and State University; Blacksburg VA 24061 USA
| | - Emmanuel A. Frimpong
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; Blacksburg VA 24061 USA
| | - Michael H. Hoff
- Fisheries Program; United States Fish and Wildlife Service; Bloomington MN 55437 USA
| | - Reuben P. Keller
- Institute of Environmental Sustainability; Loyola University Chicago; Chicago IL 60660 USA
| | - Nicholas E. Mandrak
- Department of Biological Sciences; University of Toronto Scarborough; Toronto ON M1C 1A4 Canada
| | | | - Julian D. Olden
- School of Aquatic and Fishery Sciences; University of Washington; Seattle WA 98195 USA
| | - Christina M. Romagosa
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 32611 USA
| | - David M. Lodge
- Department of Biological Sciences and Notre Dame Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| |
Collapse
|
25
|
Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL, Mahon AR, Pfrender ME, Lamberti GA, Lodge DM. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour 2015; 16:29-41. [PMID: 26032773 PMCID: PMC4744776 DOI: 10.1111/1755-0998.12433] [Citation(s) in RCA: 258] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/19/2015] [Accepted: 05/26/2015] [Indexed: 02/03/2023]
Abstract
Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206-L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina-sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.
Collapse
Affiliation(s)
- Nathan T Evans
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Brett P Olds
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Mark A Renshaw
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Cameron R Turner
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Yiyuan Li
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Christopher L Jerde
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Andrew R Mahon
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, 190 Brooks Hall, Mount Pleasant, MI, 48859, USA
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - Gary A Lamberti
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| | - David M Lodge
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
| |
Collapse
|
26
|
Egan SP, Grey E, Olds B, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy. Environ Sci Technol 2015; 49:4113-4121. [PMID: 25686279 DOI: 10.1021/es5058659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.
Collapse
Affiliation(s)
- Scott P Egan
- †Department of BioSciences, Rice University, Houston, Texas 77005, United States
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Erin Grey
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ∥College of Science, Governors State University, University Park, Illinois 60484, United States
| | - Brett Olds
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeffery L Feder
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven T Ruggiero
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carol E Tanner
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David M Lodge
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
27
|
Zeng Y, Chong KY, Grey EK, Lodge DM, Yeo DCJ. Disregarding human pre-introduction selection can confound invasive crayfish risk assessments. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0881-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
28
|
Wittmann ME, Cooke RM, Rothlisberger JD, Rutherford ES, Zhang H, Mason DM, Lodge DM. Use of structured expert judgment to forecast invasions by bighead and silver carp in Lake Erie. Conserv Biol 2015; 29:187-97. [PMID: 25132396 DOI: 10.1111/cobi.12369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/20/2014] [Indexed: 05/23/2023]
Abstract
Identifying which nonindigenous species will become invasive and forecasting the damage they will cause is difficult and presents a significant problem for natural resource management. Often, the data or resources necessary for ecological risk assessment are incomplete or absent, leaving environmental decision makers ill equipped to effectively manage valuable natural resources. Structured expert judgment (SEJ) is a mathematical and performance-based method of eliciting, weighting, and aggregating expert judgments. In contrast to other methods of eliciting and aggregating expert judgments (where, for example, equal weights may be assigned to experts), SEJ weights each expert on the basis of his or her statistical accuracy and informativeness through performance measurement on a set of calibration variables. We used SEJ to forecast impacts of nonindigenous Asian carp (Hypophthalmichthys spp.) in Lake Erie, where it is believed not to be established. Experts quantified Asian carp biomass, production, and consumption and their impact on 4 fish species if Asian carp were to become established. According to experts, in Lake Erie Asian carp have the potential to achieve biomass levels that are similar to the sum of biomasses for several fishes that are harvested commercially or recreationally. However, the impact of Asian carp on the biomass of these fishes was estimated by experts to be small, relative to long term average biomasses, with little uncertainty. Impacts of Asian carp in tributaries and on recreational activities, water quality, or other species were not addressed. SEJ can be used to quantify key uncertainties of invasion biology and also provide a decision-support tool when the necessary information for natural resource management and policy is not available.
Collapse
Affiliation(s)
- Marion E Wittmann
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46656, U.S.A..
| | | | | | | | | | | | | |
Collapse
|
29
|
Renshaw MA, Olds BP, Jerde CL, McVeigh MM, Lodge DM. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol Ecol Resour 2015; 15:168-76. [PMID: 24834966 PMCID: PMC4312482 DOI: 10.1111/1755-0998.12281] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
Abstract
Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol-chloroform-isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction.
Collapse
Affiliation(s)
- Mark A Renshaw
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| | | | | | | | | |
Collapse
|
30
|
Sargent LW, Lodge DM. Evolution of invasive traits in nonindigenous species: increased survival and faster growth in invasive populations of rusty crayfish (Orconectes rusticus). Evol Appl 2014; 7:949-61. [PMID: 25469173 PMCID: PMC4211724 DOI: 10.1111/eva.12198] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/07/2014] [Indexed: 11/28/2022] Open
Abstract
The importance of evolution in enhancing the invasiveness of species is not well understood, especially in animals. To evaluate evolution in crayfish invasions, we tested for differences in growth rate, survival, and response to predators between native and invaded range populations of rusty crayfish (Orconectes rusticus). We hypothesized that low conspecific densities during introductions into lakes would select for increased investment in growth and reproduction in invasive populations. We reared crayfish from both ranges in common garden experiments in lakes and mesocosms, the latter in which we also included treatments of predatory fish presence and food quality. In both lake and mesocosm experiments, O. rusticus from invasive populations had significantly faster growth rates and higher survival than individuals from the native range, especially in mesocosms where fish were present. There was no influence of within-range collection location on growth rate. Egg size was similar between ranges and did not affect crayfish growth. Our results, therefore, suggest that growth rate, which previous work has shown contributes to strong community-level impacts of this invasive species, has diverged since O. rusticus was introduced to the invaded range. This result highlights the need to consider evolutionary dynamics in invasive species mitigation strategies.
Collapse
Affiliation(s)
- Lindsey W Sargent
- Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
| | - David M Lodge
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame Notre Dame, IN, USA
| |
Collapse
|
31
|
Cooke RM, Wittmann ME, Lodge DM, Rothlisberger JD, Rutherford ES, Zhang H, Mason DM. Out-of-sample validation for structured expert judgment of Asian carp establishment in Lake Erie. Integr Environ Assess Manag 2014; 10:522-8. [PMID: 25044130 PMCID: PMC4285203 DOI: 10.1002/ieam.1559] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/23/2014] [Accepted: 06/30/2014] [Indexed: 05/24/2023]
Abstract
Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called a decision maker) of experts' distributions, with weights derived from performance on a set of calibration variables from the experts' field, exhibits greater statistical accuracy and greater informativeness than simple averaging with equal weights. New methods of cross validation are applied and suggest that performance characteristics relative to equal weighting could be predicted with a small number (1-2) of calibration variables. The performance-based decision maker is somewhat degraded on out-of-sample prediction, but remained superior to the equal weight decision maker in terms of statistical accuracy and informativeness.
Collapse
Affiliation(s)
- Roger M Cooke
- Resources for the Future, Washington, DC, USA; University of Strathclyde, Glasgow, Scotland, United Kingdom; Delft University of Technology, Delft, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
32
|
Affiliation(s)
- Cameron R. Turner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Matthew A. Barnes
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
| | - Charles C. Y. Xu
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Stuart E. Jones
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Christopher L. Jerde
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
| | - David M. Lodge
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
- Environmental Change Initiative University of Notre Dame Notre Dame IN 46556 USA
| |
Collapse
|
33
|
Barnes MA, Jerde CL, Wittmann ME, Chadderton WL, Ding J, Zhang J, Purcell M, Budhathoki M, Lodge DM. Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models. Ecol Evol 2014; 4:2584-93. [PMID: 25360288 PMCID: PMC4203300 DOI: 10.1002/ece3.1120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/23/2022] Open
Abstract
Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the performance of species distribution models. We assessed the importance of geographical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North American distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also compared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well-documented species like H. verticillata, missing records from single countries or ecoregions may minimally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide predictions. Regardless of focal species, we recommend that future species distribution modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under-reported and unexplored native ranges.
Collapse
Affiliation(s)
- Matthew A Barnes
- Environmental Change Initiative, University of Notre Dame Notre Dame, Indiana
| | - Christopher L Jerde
- Environmental Change Initiative, University of Notre Dame Notre Dame, Indiana
| | - Marion E Wittmann
- Environmental Change Initiative, University of Notre Dame Notre Dame, Indiana
| | | | - Jianqing Ding
- Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China
| | - Jialiang Zhang
- Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China
| | - Matthew Purcell
- Agricultural Research Service, Australian Biological Control Laboratory, United States Department of Agriculture Brisbane, Queensland, Australia
| | - Milan Budhathoki
- Center for Research Computing, University of Notre Dame Notre Dame, Indiana
| | - David M Lodge
- Environmental Change Initiative, University of Notre Dame Notre Dame, Indiana
| |
Collapse
|
34
|
Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Technol 2014; 48:1819-27. [PMID: 24422450 DOI: 10.1021/es404734p] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.
Collapse
Affiliation(s)
- Matthew A Barnes
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | | | | | | | | | | |
Collapse
|
35
|
Egan SP, Barnes MA, Hwang CT, Mahon AR, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid Invasive Species Detection by Combining Environmental DNA with Light Transmission Spectroscopy. Conserv Lett 2013. [DOI: 10.1111/conl.12017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Scott P. Egan
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| | - Matthew A. Barnes
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
| | - Ching-Ting Hwang
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - Andrew R. Mahon
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Biology and Institute for Great Lakes Research; Central Michigan University; Mount Pleasant MI 48859 USA
| | - Jeffery L. Feder
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| | - Steven T. Ruggiero
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - Carol E. Tanner
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Department of Physics; University of Notre Dame; Notre Dame IN 46556 USA
| | - David M. Lodge
- Department of Biological Sciences; University of Notre Dame; Notre Dame IN 46556 USA
- Advanced Diagnostics and Therapeutics Initiative; University of Notre Dame; Notre Dame IN 46556 USA
- Environmental Change Initiative; University of Notre Dame; Notre Dame IN 46556 USA
| |
Collapse
|
36
|
Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLoS One 2013; 8:e58316. [PMID: 23472178 PMCID: PMC3589332 DOI: 10.1371/journal.pone.0058316] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/01/2013] [Indexed: 11/19/2022] Open
Abstract
In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.
Collapse
Affiliation(s)
- Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan, USA.
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Lodge DM, Deines A, Gherardi F, Yeo DC, Arcella T, Baldridge AK, Barnes MA, Chadderton WL, Feder JL, Gantz CA, Howard GW, Jerde CL, Peters BW, Peters JA, Sargent LW, Turner CR, Wittmann ME, Zeng Y. Global Introductions of Crayfishes: Evaluating the Impact of Species Invasions on Ecosystem Services. Annu Rev Ecol Evol Syst 2012. [DOI: 10.1146/annurev-ecolsys-111511-103919] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Impacts of nonindigenous crayfishes on ecosystem services exemplify the mixture of positive and negative effects of intentionally introduced species. Global introductions for aquaculture and ornamental purposes have begun to homogenize naturally disjunct global distributions of crayfish families. Negative impacts include the loss of provisioning (e.g., reductions in edible native species, reproductive interference or hybridization with native crayfishes), regulatory (e.g., lethal disease spread, increased costs to agriculture and water management), supporting (e.g., large changes in ecological communities), and cultural (e.g., loss of festivals celebrating native crayfish) services. Where quantification of impacts exists (e.g., Procambarus clarkii and Pacifastacus leniusculus in Europe), regulations now prohibit introduction and spread of crayfishes, indicating that losses of ecosystem services have outweighed gains. Recent research advances such as predicting invasiveness, predicting spread, improved detection and control, and bioeconomic analysis to increase cost-effectiveness of management could be employed to reduce future losses of ecosystem services.
Collapse
Affiliation(s)
- David M. Lodge
- Environmental Change Initiative and
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Andrew Deines
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Francesca Gherardi
- Dipartimento di Biologia Evoluzionistica “Leo Pardi,” Università degli Studi di Firenze, 50136 Firenze, Italy
| | - Darren C.J. Yeo
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Tracy Arcella
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ashley K. Baldridge
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Matthew A. Barnes
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | | | - Jeffrey L. Feder
- Environmental Change Initiative and
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Crysta A. Gantz
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Geoffrey W. Howard
- Invasive Species Initiative, International Union for Conservation of Nature Species Program, Nairobi 00200, Kenya
| | - Christopher L. Jerde
- Environmental Change Initiative and
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | | | - Jody A. Peters
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Lindsey W. Sargent
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Cameron R. Turner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Marion E. Wittmann
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Yiwen Zeng
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| |
Collapse
|
38
|
Mahon AR, Barnes MA, Li F, Egan SP, Tanner CE, Ruggiero ST, Feder JL, Lodge DM. DNA-based species detection capabilities using laser transmission spectroscopy. J R Soc Interface 2012; 10:20120637. [PMID: 23015524 PMCID: PMC3565792 DOI: 10.1098/rsif.2012.0637] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.
Collapse
Affiliation(s)
- A R Mahon
- 1Department of Biology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Affiliation(s)
- D M Lodge
- Dept of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
40
|
Lodge DM, Turner CR, Jerde CL, Barnes MA, Chadderton L, Egan SP, Feder JL, Mahon AR, Pfrender ME. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol 2012; 21:2555-8. [PMID: 22624944 PMCID: PMC3412215 DOI: 10.1111/j.1365-294x.2012.05600.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.
Collapse
Affiliation(s)
- David M Lodge
- Environmental Change Initiative, University of Notre Dame, Notre Dame, IN 46556, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Jerde CL, Miller DJ, Mahon AR, Chadderton WL, Lodge DM. Response to Casey et al.'s sensitivity of detecting environmental DNA comment. Conserv Lett 2012; 5:241-242. [DOI: 10.1111/j.1755-263x.2012.00231.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
|
42
|
Drury KLS, Lodge DM. Combining perturbations and parameter variation to influence mean first passage times. Bull Math Biol 2012; 74:1606-28. [PMID: 22538978 DOI: 10.1007/s11538-012-9727-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 04/03/2012] [Indexed: 11/26/2022]
Abstract
Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilibrium number, showing that both competition and predation rates in this model are bifurcating parameters. We then introduce a stochastic process to model the effects of population perturbations. We demonstrate how to evaluate the joint effects of perturbations and drift using the common currency of mean first passage time to transitions between stable states. Our methods and results are quite general, and for example, can relate to issues in both pest control and sustainable harvest. Our results show that parameter drift (1) does not importantly change the expected time to reach target points within a basin of attraction, but (2) can dramatically change the expected time to shift between basins of attraction, through its effects on equilibrium resilience.
Collapse
Affiliation(s)
- Kevin L S Drury
- Department of Mathematics, Bethel College, Mishawaka, IN 46545, USA.
| | | |
Collapse
|
43
|
|
44
|
Li F, Mahon AR, Barnes MA, Feder J, Lodge DM, Hwang CT, Schafer R, Ruggiero ST, Tanner CE. Quantitative and rapid DNA detection by laser transmission spectroscopy. PLoS One 2011; 6:e29224. [PMID: 22195026 PMCID: PMC3241715 DOI: 10.1371/journal.pone.0029224] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 11/22/2011] [Indexed: 12/11/2022] Open
Abstract
Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications.
Collapse
Affiliation(s)
- Frank Li
- Department of Physics, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Andrew R. Mahon
- Department of Biological Sciences and Center for Aquatic Conservation, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan, United States of America
| | - Matthew A. Barnes
- Department of Biological Sciences and Center for Aquatic Conservation, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jeffery Feder
- Department of Biological Sciences and Center for Aquatic Conservation, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David M. Lodge
- Department of Biological Sciences and Center for Aquatic Conservation, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Ching-Ting Hwang
- Department of Physics, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences and Center for Aquatic Conservation, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Robert Schafer
- Department of Physics, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Steven T. Ruggiero
- Department of Physics, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Carol E. Tanner
- Department of Physics, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
| |
Collapse
|
45
|
Chapin FS, Power ME, Pickett STA, Freitag A, Reynolds JA, Jackson RB, Lodge DM, Duke C, Collins SL, Power AG, Bartuska A. Earth Stewardship: science for action to sustain the human-earth system. Ecosphere 2011. [DOI: 10.1890/es11-00166.1] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
46
|
Abstract
The effects of non-native invasive species are costly and environmentally damaging, and resources to slow their spread and reduce their effects are scarce. Models that accurately predict where new invasions will occur could guide the efficient allocation of resources to slow colonization. We assessed the accuracy of a model that predicts the probability of colonization of lakes in Wisconsin by Eurasian watermilfoil (Myriophyllum spicatum). We based this predictive model on 9 years (1990-1999) of sequence data of milfoil colonization of lakes larger than 25 ha (n =1803). We used milfoil colonization sequence data from 2000 to 2006 to test whether the model accurately predicted the number of lakes that actually were colonized from among the 200 lakes identified as being most likely to be colonized. We found that a lake's predicted probability of colonization was not correlated with whether a lake actually was colonized. Given the low predictability of colonization of specific lakes, we compared the efficacy of preventing milfoil from leaving occupied sites, which does not require predicting colonization probability, with protecting vacant sites from being colonized, which does require predicting colonization probability. Preventing organisms from leaving colonized sites reduced the likelihood of spread more than protecting vacant sites. Although we focused on the spread of a single species in a particular region, our results show the shortcomings of gravity models in predicting the spread of numerous non-native species to a variety of locations via a wide range of vectors.
Collapse
Affiliation(s)
- John D Rothlisberger
- Center for Aquatic Conservation and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, U.S.A.
| | | |
Collapse
|
47
|
|
48
|
Keller RP, Drake JM, Drew MB, Lodge DM. Linking environmental conditions and ship movements to estimate invasive species transport across the global shipping network. DIVERS DISTRIB 2010. [DOI: 10.1111/j.1472-4642.2010.00696.x] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
49
|
Yeo DCJ, Ahyong ST, Lodge DM, Ng PKL, Naruse T, Lane DJW. Semisubmersible oil platforms: understudied and potentially major vectors of biofouling-mediated invasions. Biofouling 2010; 26:179-186. [PMID: 19927240 DOI: 10.1080/08927010903402438] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biofouling has long been recognised as a major pathway for the introduction of non-indigenous species. This study records the decapods and stomatopod crustaceans fouling a semisubmersible oil platform dry docked for hull cleaning in Jurong Port, Singapore. Of the 25 species of decapods identified, 13 were non-indigenous and represent new records to Singapore waters. Of these, the crabs Glabropilumnus seminudus and Carupa tenuipes are known to be invasive in other parts of the world. The stomatopod, Gonodactylaceus randalli, is the first mantis shrimp recorded in a biofouling community. The richness and diversity of this fouling community, consisting of many vagile species, highlights the difference between platforms and ships. With the expansion of maritime oil and gas exploration, the threat posed by an expanded fleet of semisubmersible oil platforms translocating non-indigenous fouling communities across biogeographical boundaries is very serious. Scientists, policy-makers, and stakeholders should turn their attention to this growing problem.
Collapse
Affiliation(s)
- Darren C J Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore.
| | | | | | | | | | | |
Collapse
|
50
|
|