ДНК окружающей среды как инструмент изучения видового разнообразия и экологии птиц

С.А. Галкина, И.В. Демина, Е.В. Платонова, О.Д. Такки и А.Г. Демин

Труды Зоологического института РАН, 2025, 329(2): 170–186   ·   https://doi.org/10.31610/trudyzin/2025.329.2.170

Полный текст  

Резюме

Птицы играют ключевую роль в функционировании большинства крупных экосистем планеты и являются важными объектами биомониторинга. Традиционные методы их изучения нередко имеют ограничения, особенно при исследовании редких, скрытных, мигрирующих видов или видов, обитающих в труднодоступных местах. Сложности с организацией полевых наблюдений, плохие погодные условия и разница в квалификации специалистов могут существенно искажать получаемые данные или даже делать их анализ невозможным. ДНК окружающей среды (экологическая ДНК, эДНК, environmental DNA, eDNA) – это неинвазивный и высокопроизводительный инструмент оценки биоразнообразия, который постепенно входит в практику экологических исследований по всему миру. Наиболее впечатляющие результаты его применения связаны с изучением ихтиофауны, однако в последние несколько лет анализ эДНК также стал использоваться в орнитологии. Тем не менее, целенаправленные исследования птиц с применением эДНК проводятся сравнительно редко, что связано с отсутствием достаточной апробации методик. Актуальные данные (по состоянию на начало 2025 г.) позволяют утверждать, что эДНК может стать ценным инструментом для изучения биоразнообразия и экологии птиц. Методы, основанные на анализе эДНК, уже доказали свою эффективность в обнаружении водоплавающих и околоводных птиц, а также видов, не связанных с водной средой, например птиц-опылителей. В данной статье представлен обзор применения метода эДНК для детекции птиц в различных экосистемах – от тропических лесов до полярных широт, включая как водные, так и наземные среды. Рассматриваются основные направления использования метода, такие как идентификация отдельных видов и оценка разнообразия авифауны. Особое внимание уделяется меташтрихкодированию эДНК как наиболее перспективному подходу, способному значительно повысить производительность биомониторинговых исследований птиц.

Ключевые слова

биоразнообразие, ДНК окружающей среды, ДНК-штрихкоды, меташтрихкодирование, Aves, eDNA

Поступила в редакцию 30 января 2024 г.  ·  Принята в печать 29 апреля 2025 г.  ·  Опубликована 3 июня 2025 г.

Литература

Allen M.C., Kwait R., Vastano A., Kisurin A., Zoccolo I., Jaffe B.D., Angle J.C., Maslo B. and Lockwood J.L. 2023. Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals. Scientific Reports, 13: 180. https://doi.org/10.1038/s41598-023-27512-8

Banchi E., Pallavicini A. and Muggia L. 2020. Relevance of plant and fungal DNA metabarcoding in aerobiology. Aerobiologia, 36(1): 9–23. https://doi.org/10.1007/s10453-019-09574-2

Barnes M.A., Turner C.R., Jerde C.L., Renshaw M.A., Chadderton W.L. and Lodge D.M. 2014. Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology, 48: 1819–1827. https://doi.org/10.1021/es404734p

Beng K.C. and Corlett R.T. 2020. Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects. Biodiversity and Conservation, 29: 2089–2121. https://doi.org/10.1007/s10531-020-01980-0

Blake M., McKeown N.J., Bushell M.L. and Shaw P.W. 2016. DNA extraction from spider webs. Conservation Genetics Resources, 8: 219–221. https://doi.org/10.1007/s12686-016-0537-8

Brav-Cubitt T. and Middleton D.M.R.L. 2024. A real-time PCR assay for detecting trace amounts of kiwi (Apteryx spp.) DNA. Conservation Genetics Resources. https://doi.org/10.1007/s12686-024-01371-5

Chabot D. and Francis C.M. 2016. Computer-automated bird detection and counts in high-resolution aerial images: a review. Journal of Field Ornithology, 87(4): 343–359. https://doi.org/10.1111/jofo.12171

Clare E.L., Economou C.K., Faulkes C.G., Gilbert J.D., Bennett F., Drinkwater R. and Littlefair J.E. 2021. eDNAir: proof of concept that animal DNA can be collected from air sampling. PeerJ, 9: e11030. https://doi.org/10.7717/peerj.11030

Clare E.L., Economou C.K., Bennett F.J., Dyer C.E., Adams K., McRobie B., Drinkwater R. and Littlefair J.E. 2022. Measuring biodiversity from DNA in the air. Current Biology, 32: 693–700. e5. https://doi.org/10.1016/j.cub.2021.11.064

Closek C.J., Santora J.A., Starks H.A., Schroeder I.D., Andruszkiewicz E.A., Sakuma K.M., Bograd S.J., Hazen E.L., Field J.C. and Boehm A.B. 2019. Marine vertebrate biodiversity and distribution within the central California Current using environmental DNA (eDNA) metabarcoding and ecosystem surveys. Frontiers in Marine Science, 6: 732. https://doi.org/10.3389/fmars.2019.00732

David B.O., Fake D.R., Hicks A.S., Wilkinson S.P., Bunce M., Smith J.S., West D.W., Collins K.E. and Gleeson D.M. 2021. Sucked in by eDNA – a promising tool for complementing riverine assessment of freshwater fish communities in Aotearoa New Zealand. New Zealand Journal of Zoology, 48: 217–244. https://doi.org/10.1080/03014223.2021.1905672

Davy C.M., Kidd A.G. and Wilson C.C. 2015. Development and validation of environmental DNA (eDNA) markers for detection of freshwater turtles. PloS ONE, 10(7): e0130965. https://doi.org/10.1371/journal.pone.0130965

Day K., Campbell H., Fisher A., Gibb K., Hill B., Rose A. and Jarman S.N. 2019. Development and validation of an environmental DNA test for the endangered Gouldian finch. Endangered Species Research, 40: 171–182. https://doi.org/10.3354/esr00987

Dejean T., Valentini A., Duparc A., Pellier-Cuit S., Pompanon F., Taberlet P. and Miaud C. 2011. Persistence of environmental DNA in freshwater ecosystems. PLoS ONE, 6(8): e23398. https://doi.org/10.1371/journal.pone.0023398

Dickie I.A., Boyer S., Buckley H.L., Duncan R.P., Gardner P.P., Hogg I.D., Holdaway R.J., Lear G., Makiola A., Morales S.E., Powell J.R. and Weaver L. 2018. Towards robust and repeatable sampling methods in eDNA-based studies. Molecular Ecology Resources, 18(5): 940–952. https://doi.org/10.1111/1755-0998.12907

Dysthe J.C., Franklin T.W., McKelvey K.S., Young M.K. and Schwartz M.K. 2018. An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I. PLoS ONE, 13(11): e0206851. https://doi.org/10.1371/jour-nal.pone.0206851

Feist S.M., Guan X., Malmfeldt M.P. and Lance R.F. 2022. Two novel qPCR assays to enhance black rail (Laterallus jamaicensis) eDNA surveys in the United States. Conservation Genetics Resources, 14: 321–329. https://doi.org/10.1007/s12686-022-01279-y

Foote A.D., Thomsen P.F., Sveegaard S., Wahlberg M., Kielgast J., Kyhn L.A., Salling A.B., Galatius A., Orlando L. and Gilbert M.T.P. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE, 7: e41781. https://doi.org/10.1371/journal.pone.0041781

Fraija-Fernández N., Bouquieaux M.C., Rey A., Mendibil I., Cotano U., Irigoien X., Santos M. and Rodríguez-Ezpeleta N. 2020. Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area. Ecology and Evolution, 10: 7560–7584. https://doi.org/10.1002/ece3.6482

Fraixedas S., Linden A., Piha M., Cabeza M., Gregory R. and Lehikoinen A. 2020. A state-of-the-art review on birds as indicators of biodiversity: Advances, challenges, and future directions. Ecological Indicators, 118: 106728. https://doi.org/10.1016/j.ecolind.2020.106728

Frolov A.V., Vishnevskaya M.S., Viljanen H., Montreuil O. and Akhmetova L.A. 2024. New data on trophic associations of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) and lemurs (Primates, Lemuroidea) in Madagascar revealed by metabarcoding. Biodiversity Data Journal, 12: e130400. https://doi.org/10.3897/BDJ.12.e130400

Furlan E.M., Gleeson D., Hardy C.M. and Duncan R.P. 2016. A framework for estimating the sensitivity of eDNA surveys. Molecular Ecology Resources, 16(3): 641–654. https://doi.org/10.1111/1755-0998.12483

Furness R.W. and Greenwood J.J. 1993. Birds as monitors of environmental change. Springer, London, 356 p. https://doi.org/10.1007/978-94-015-1322-7

Garrett N.R., Watkins J., Simmons N.B., Fenton B., Maeda-Obregon A., Sanchez D.E., Froehlich E.M., Walker F.M., Littlefair J.E. and Clare E.L. 2023. Airborne eDNA documents a diverse and ecologically complex tropical bat and other mammal community. Environmental DNA, 5: 350–362. https://doi.org/10.1002/edn3.385

Gregorič M., Kutnjak D., Bačnik K., Gostinčar C., Pecman A., Ravnikar M. and Kuntner M. 2022. Spider webs as eDNA samplers: Biodiversity assessment across the tree of life. Molecular ecology resources, 22(7): 2534–2545. https://doi.org/10.1111/1755-0998.13629

Gregory R.D., van Strien A., Vorisek P., Gmelig Meyling A.W., Noble D.G., Foppen R.P. and Gibbons D.W. 2005. Developing indicators for European birds. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 360(1454): 269–288. https://doi.org/10.1098/rstb.2004.1602

Guthrie A.M., Cooper C.E., Bateman P.W., van der Heyde M., Allentoft M.E. and Nevill P. 2024. A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light, and temperature. Environmental DNA, 6: e581. https://doi.org/10.1002/edn3.581

Haderlé R., Bouveret L., Chazal J., Girardet J., Iglésias S., Lopez P.J., Millon C., Valentini A., Ung V. and Jung J.L. 2024. eDNA-based survey of the marine vertebrate biodiversity off the west coast of Guadeloupe (French West Indies). Biodiversity Data Journal, 12: e125348. https://doi.org/10.3897/BDJ.12.e125348

Harper L.R., Handley L.L., Hahn C., Boonham N., Rees H.C., Gough K.C., Lewis E., Adams I.P., Brotherton P., Phillips S. and Hänfling B. 2018. Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecology and Evolution, 8: 6330–6341. https://doi.org/10.1002/ece3.4013

Harrison J.B., Sunday J.M. and Rogers S.M. 2019. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings of the Royal Society, Biological sciences, 286(1915): 20191409. https://doi.org/10.1098/rspb.2019.1409

Hebert P.D.N., Cywinska A., Ball S.L. and de Waard J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, Biological Sciences, 270(1512): 313–321. https://doi.org/10.1098/rspb.2002.2218

Heert P.D., Stoeckle M.Y., Zemlak T.S. and Francis C.M. 2004. Identification of Birds through DNA Barcodes. PLoS Biology, 2(10): e312. https://doi.org/10.1371/journal.pbio.0020312

Hird S.M. 2017. Evolutionary Biology Needs Wild Microbiomes. Frontiers in Microbiology, 8: 725. https://doi.org/10.3389/fmicb.2017.00725

Honka J., Kvist L., Øien I.J., Aarvak T., Siivonen S. and Aspi J. 2024a. Environmental DNA reveals a presence of Anser fabalis (Bean Goose) and an absence of Anser erythropus (Lesser Whitefronted Goose) in Finnish Northern Lapland. Ornithological Applications, 127(1): 1–10. https://doi.org/10.1093/ornithapp/duae060

Honka J., Kvist L., Olli S., Laaksonen T. and Aspi J. 2024b. Optimised PCR assays for detecting elusive waterfowl from environmental DNA. Ecology and Evolution, 14: e11224. https://doi.org/10.1002/ece3.11224

Ilina A.V., Galkina S.A., Starikov D.A., Salhabeev R.G. and Dyomin A.G. 2024. Study on exogenous DNA degradation in Ladoga lake water. Biotekhnologiya, 40(3): 100–108. [In Russian]. https://doi.org/10.56304/S0234275824030116

Jensen M.R., Høgslund S., Knudsen S.W., Nielsen J., Møller P.R., Rysgaard S. and Thomsen P.F. 2023. Distinct latitudinal community patterns of Arctic marine vertebrates along the East Greenlandic coast detected by environmental DNA. Diversity and Distributions, 29: 316–334. https://doi.org/10.1111/ddi.13665

Jerde C.L., Mahon A.R., Chadderton W.L. and Lodge D.M. 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation letters, 4(2): 150–157. https://doi.org/10.1111/j.1755-263x.2010.00158.x

Jo T.S., Tsuri K. and Yamanaka H. 2022. Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance? Naturwissenschaften, 109(4): 38. https://doi.org/10.1007/s00114-022-01808-7

Johnson M.D., Barnes M.A., Garrett N.R. and Clare E.L. 2023. Answers blowing in the wind: Detection of birds, mammals, and amphibians with airborne environmental DNA in a natural environment over a yearlong survey. Environmental DNA, 5(2): 375–387. https://doi.org/10.1002/edn3.388

Jønsson K.A., Thomassen E.E., Iova B., Sam K. and Thomsen P.F. 2023. Using environmental DNA to investigate avian interactions with flowering plants. Environmental DNA, 5: 462–475. https://doi.org/10.1002/edn3.393

Katayama N., Yamamoto S., Baba Y.G., Ito K. and Yamasako J. 2024. Complementary role of environmental DNA for line-transect bird surveys: A field test in a Japanese rice landscape. Ecological Indicators, 166: 112442. https://doi.org/10.1016/j.ecolind.2024.112442

Katz A.D., Harper L.R., Sternhagen E.C., Pearce S.E., Melder C.A., Sperry J.H. and Davis M.A. 2021. Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni). Environmental DNA, 3: 409–425. https://doi.org/10.1002/edn3.126

Kerley G., Landman M., Ficetola G.F., Boyer F., Bonin A., Rioux D., Taberlet P. and Coissac E. 2018. Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories. Oecologia, 188: 29961180. https://doi.org/10.1007/s00442-018-4203-6

Kirchgeorg S., Chang J.J.M., Ip Y.C.I., Jucker M., Geckeler C., Lüthi M., van der Loo E., Mächler E., Franco-Sierra N.D., Herrera M.A.G., Pellissier L., Deiner K., Desiderato A. and Mintchev S. 2024. eProbe: sampling of environmental DNA within tree canopies with drones. Environmental Science and Technology, 58(37): 16410–16420. https://doi.org/10.1021/acs.est.4c05595

Koskimies P. 1989. Birds as a tool in environmental monitoring. Annales Zoologici Fennici, 26(3): 153–166.

Lacoursière-Roussel A., Dubois Y., Normandeau E. and Bernatchez L. 2016. Improving herpetological surveys in eastern North America using the environmental DNA method. Genome, 59(11): 991–1007. https://doi.org/10.1139/gen-2015-0218

Le Maho Y., Karmann H., Briot D., Handrich Y., Robin J.P., Mioskowski E., Cherel Y. and Farni J. 1992. Stress in birds due to routine handling and a technique to avoid it. The American journal of physiology, 263(4 Pt 2): R775–R781. https://doi.org/10.1152/ajpregu.1992.263.4.R775

Lodge D., Turner C., Jerde C., Barnes M.A., Chadderton L., Egan S.P., Feder J.L., Mahon A.R. and Pfrender M.E. 2012. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology, 11: 2555–2558. https://doi.org/10.1111/j.1365-294X.2012.05600.x

Lodge D.M. 2024. Conservation in a litre of air. Molecular Ecology Resources, 24(1): e13883. https://doi.org/10.1111/1755-0998.13883

Lozano Mojica J.D. and Caballero S. 2021. Applications of eDNA metabarcoding for vertebrate diversity studies in northern Colombian water bodies. Frontiers in Ecology and Evolution, 8: 617948. https://doi.org/10.3389/fevo.2020.617948

Lynggaard C., Bertelsen M.F., Jensen C.V., Johnson M.S., Frøslev T.G., Olsen M.T. and Bohmann K. 2022. Airborne environmental DNA for terrestrial vertebrate community monitoring. Current Biology, 32(3): 701–707. https://doi.org/10.1016/j.cub.2021.12.014

Lynggaard C., Frøslev T.G., Johnson M.S., Olsen M.T. and Bohmann K. 2024. Airborne environmental DNA captures terrestrial vertebrate diversity in nature. Molecular Ecology Resources, 24(1): e13840. https://doi.org/10.1111/1755-0998.13840

Macher T.-H., Schütz R., Arle J., Beermann A.J., Koschorreck J., Leese F. 2021. Beyond fish eDNA metabarcoding: field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics, 5: e66557. https://doi.org/10.3897/mbmg.5.66557

Mariani S., Harper L.R., Collins R.A., Baillie C., Wangensteen O.S., McDevitt A.D., Heddell-Cowie M. and Genner M.J. 2021. Estuarine molecular bycatch as a landscape-wide biomonitoring tool. Biological Conservation, 261: 109287. https://doi.org/10.1016/j.biocon.2021.109287

McDonald R., Bateman P.W., Cooper C., van der Heyde M., Mousavi-Derazmahalleh M., Hedges B.A., Guzik M.T. and Nevill P. 2023. Detection of vertebrates from natural and artificial inland water bodies in a semiarid habitat using eDNA from filtered, swept, and sediment samples. Ecology and Evolution, 13: e10014. https://doi.org/10.1002/ece3.10014

Mena J.L., Yagui H., Tejeda V., Bonifaz E., Bellemain E., Valentini A., Tobler M.W., Sánchez-Vendizú P. and Lyet A. 2021. Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests. Ecological Applications, 31(5): e02335. https://doi.org/10.1002/eap.2335

Miaud C., Taberlet P. and Dejean T. 2012. ADN “environnemental”: un saut méthodologique pour les inventaires de la biodiversité. Sciences Eaux and Territoires, 6: 92–95. https://doi.org/10.14758/SET-REVUE.2012.6.16

Miya M. 2022. Environmental DNA metabarcoding: a novel method for biodiversity monitoring of marine fish communities. Annual Review of Marine Science, 14: 161–185. https://doi.org/10.1146/annurev-marine-041421-082251

Miyata K., Inoue Y., Amano Y., Nishioka T., Yamane M., Kawaguchi T., Morita O. and Honda H. 2021. Fish environmental RNA enables precise ecological surveys with high positive predictivity. Ecological Indicators, 128: 107796. https://doi.org/10.1016/j.ecolind.2021.107796

Monge O., Dumas D. and Baus I. 2020. Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. Conservation Genetics Resources, 12: 131–139. https://doi.org/10.1007/s12686-018-1074-4

Mokievsky V.O., Tsetlin A.B., Azovsky A.I., Naumov A.D., Kosobokova K.N., Kuzishchin K.V., Sapozhnikov F.V., Vedenin A.A., Gavrilo M.V., Isachenko A.I., Ilyushin D.G., Simakova U.V., Zalota A.K., Shabalin N.V., Maksimova O.V., Glazov D.M., Mardashova M.V., Kalinina O.Yu., Valieva A.S., Zagretdinova D.R., Lazareva R.E. and Udovik D.A. 2020. Species as biological indicators of the state of marine arctic ecosystems. NIR Foundation, Moscow, 383 p. [In Russian].

Muff M., Jaquier M., Marques V., Ballesta L., Deter J., Bockel T., Hocdé R., Juhel J.B., Boulanger E., Guellati N., Fernández A.P., Valentini A., Dejean T., Manel S., Albouy C., Durville P., Mouillot D., Holon F. and Pellissier L. 2023. Environmental DNA highlights fish biodiversity in mesophotic ecosystems. Environmental DNA, 5(1): 56–72. https://doi.org/10.1002/edn3.358

Neice A.A. and McRae S.B. 2021. An eDNA diagnostic test to detect a rare, secretive marsh bird. Global Ecology and Conservation, 27: e01529. https://doi.org/10.1016/j.gecco.2021.e01529

Newton J.P., Bateman P.W., Heydenrych M.J., Kestel J.H., Dixon K.W., Prendergast K.S., White N.E. and Nevill P. 2023. Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant-animal interactions. Environmental DNA, 5: 488–502. https://doi.org/10.1002/edn3.399

Newton J.P., Nevill P., Bateman P.W., Campbell M.A. and Allentoft M.E. 2024. Spider webs capture environmental DNA from terrestrial vertebrates. iScience, 27(2): 108904. https://doi.org/10.1016/j.isci.2024.108904

Palacios Mejia M., Curd E., Edalati K., Renshaw M.A., Dunn R., Potter D., Fraga N., Moore J., Saiz J., Wayne R. and Parker S.S. 2021. The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs. Environmental DNA, 3(1): 214–230. https://doi.org/10.1002/edn3.161

Parsons K.M., Everett M., Dahlheim M. and Park L. 2018. Water, water everywhere: Environmental DNA can unlock population structure in elusive marine species. Royal Society open science, 5: 180537. https://doi.org/10.1098/rsos.180537

Pérez-Fleitas E., Milián-García Y., Sosa-Rodríguez G., Amato G., Rossi N., Shirley M.H. and Hanner R.H. 2023. Environmental DNA-based biomonitoring of Cuban Crocodylus and their accompanying vertebrate fauna from Zapata Swamp, Cuba. Scientific Reports, 13: 20438. https://doi.org/10.1038/s41598-023-47675-8

Piaggio A.J., Engeman R.M., Hopken M.W., Humphrey J.S., Keacher K.L., Bruce W.E. and Avery M.L. 2014. Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Molecular Ecology Resources, 14(2): 374–380. https://doi.org/10.1111/1755-0998.12180

Pinakhina D.V. and Chekunova E.M. 2020. Environmental DNA: history of studies, current and perspective applications in fundamental and applied research. Ecological Genetics, 18(4): 493–509. [In Russian]. https://doi.org/10.17816/ecogen25900

Polanco F.A., Mutis Martinezguerra M., Marques V., Villa-Navarro F., Borrero Pérez G.H., Cheutin M.C., Dejean T., Hocdé R., Juhel J.B., Maire E., Manel S., Spescha S., Valentini A., Mouillot D., Albouy C. and Pellissier L. 2021. Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica, 53: 1606–1619. https://doi.org/10.1111/btp.13009

Port J.A., O’Donnell J.L., Romero-Maraccini O.C., Leary P.R., Litvin S.Y., Nickols K.J., Yamahara K.M. and Kelly R.P. 2016. Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Molecular Ecology, 25: 527–541. https://doi.org/10.1111/mec.13481

Ritter C.D., Dal Pont G., Stica P.V., Horodesky A., Cozer N., Netto O.S.M., Henn C., Ostrensky A. and Pie M.R. 2022. Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch. Environmental Advances, 7: 100169. https://doi.org/10.1016/j.envadv.2022.100169

Roesma D.I., Djong H.T., Janra M.N. and Aidil D.R. 2021. Freshwater vertebrates monitoring in Maninjau Lake, West Sumatra, Indonesia using environmental DNA. Biodiversitas, 22(5): 2794–2802. https://doi.org/10.13057/biodiv/d220543

Ryan E., Bateman P., Fernandes K., van der Heyde M. and Nevill P. 2022. eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection. Environmental DNA, 4: 940–953. https://doi.org/10.1002/edn3.306

Saenz-Agudelo P., Delrieu-Trottin E., DiBattista J.D., Martínez-Rincon D., Morales-González S., Pontigo F., Ramírez P., Silva A., Soto M. and Correa C. 2022. Monitoring vertebrate biodiversity of a protected coastal wetland using eDNA metabarcoding. Environmental DNA, 4: 77–92. https://doi.org/10.1002/edn3.200

Sakata M.K., Yamamoto S., Gotoh R.O., Miya M., Yamanaka H. and Minamoto T. 2020. Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA. Environmental DNA, 2(4): 505–518. https://doi.org/10.1002/edn3.75

Schütz R., Tollrian R. and Schweinsberg M. 2020. A novel environmental DNA detection approach for the wading birds Platalea leucorodia, Recurvirostra avosettaand Tringa totanus. Conservation Genetics Resources, 12: 529–531. https://doi.org/10.1007/s12686-020-01143-x

Serrao N.R., Weckworth J.K., McKelvey K.S., Dysthe J.C. and Schwartz M.K. 2021. Molecular genetic analysis of air, water, and soil to detect big brown bats in North America. Biological Conservation, 261: 109252. https://doi.org/10.1016/j.biocon.2021.109252

Sigsgaard E.E., Nielsen I.B., Bach S.S., Lorenzen E.D., Robinson D.P., Knudsen S.W., Pedersen M.W., Jaidah M.A., Orlando L., Willerslev E., Møller P.R. and Thomsen P.F. 2016. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nature Ecology and Evolution, 1(1): 4. https://doi.org/10.1038/s41559-016-0004

Sogin M.L., Morrison H.G., Huber J.A. Mark Welch D., Huse S.M., Neal P.R., Arrieta J.M. and Herndl G.J. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proceedings of the National Academy of Sciences, 103(32): 12115–12120. https://doi.org/10.1073/pnas.0605127103

Sohn H. and Song Y. 2024. Monitoring of mammal and bird species in an urban ecological park using environmental DNA metabarcoding. Urban Ecosystems, 27: 1–14. https://doi.org/10.1007/s11252-024-01557-7

Steele B.B., Bayn R.L. and Val Grant C. 1984. Environmental monitoring using populations of birds and small mammals: Analyses of sampling effort. Biological Conservation, 30(2): 157–172. https://doi.org/10.1016/0006-3207(84)90064-8

Suarez-Bregua P., Alvarez-Gonzalez M., Parsons K.M., Rotllant J., Pierce G.J. and Saavedra C. 2022. Environmental DNA (eDNA) for monitoring marine mammals: Challenges and opportunities. Frontiers in Marine Science, 9: 987774. https://doi.org/10.3389/fmars.2022.987774

Taberlet P., Coissac E., Hajibabaei M. and Rieseberg L.H. 2012a. Environmental DNA. Molecular Ecology, 21(8): 1789–1793. https://doi.org/10.1111/j.1365-294x.2012.05542.x

Taberlet P., Coissac E., Pompanon F., Brochmann C. and Willerslev E. 2012b. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21(8): 2045–2050. https://doi.org/10.1111/j.1365-294x.2012.05470.x

Taberlet P., Bonin A., Zinger L. and Coissac E. 2018. Environmental DNA: For biodiversity research and monitoring. Oxford University Press, Oxford. https://doi.org/10.1093/oso/9780198767220.001.0001

Takahara T., Minamoto T., Yamanaka H., Doi H. and Kawabata Z. 2012. Estimation of fish biomass using environmental DNA. PLoS ONE, 7(4): e35868. https://doi.org/10.1371/journal.pone.0035868

Takahara T., Minamoto T. and Doi H. 2013. Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE, 8(2): e56584. https://doi.org/10.1371/journal.pone.0056584

Takahashi M., Saccò M., Kestel J.H., Nester G., Campbell M.A., van der Heyde M., Heydenrych M.J., Juszkiewicz D.J., Nevill P., Dawkins K.L., BesseyC., Fernandes K., Miller H., Power M., Mousavi-Derazmahalleh M., Newton J.P., White N.E., Richards Z.T. and Allentoft M.E. 2023. Aquatic environmental DNA: a review of the macro-organismal biomonitoring revolution. Science of the Total Environment, 873: 162322. https://doi.org/10.1016/j.scitotenv.2023.162322

Tetzlaff S.J., Katz A.D., Wolff P.J. and Kleitch M.E. 2024. Comparison of soil eDNA to camera traps for assessing mammal and bird community composition and site use. Ecology and Evolution, 14(7): e70022. https://doi.org/10.1002/ece3.70022

Thomsen P., Kielgast J., Iversen L., Moller P., Rasmussen M. and Willerslev E. 2012a. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7: e41732. https://doi.org/10.1371/journal.pone.0041732

Thomsen P.F., Kielgast J.O.S., Iversen L.L., Wiuf C., Rasmussen M., Gilbert M.T.P., Orlando L. and Willerslev E. 2012b. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21(11): 2565–2573. https://doi.org/10.1111/j.1365-294x.2011.05418.x

Thomsen P.F., Møller P.R., Sigsgaard E.E., Knudsen S.W., Jørgensen O.A. and Willerslev E. 2016. Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS ONE, 11: e0165252. https://doi.org/10.1371/journal.pone.0165252

Thomsen P.F. and Sigsgaard E.E. 2019. Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. Ecology and Evolution, 9(4): 1665–1679. https://doi.org/10.1002/ece3.4809

Tsuji S., Inui R., Nakao R., Miyazono S., Saito M., Kono T. and Akamatsu Y. 2022. Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community. Scientific Reports, 12: 21524. https://doi.org/10.1038/s41598-022-25274-3

Urban L., Miller L.K., Eason D., Vercoe D., Shaffer M., Wilkinson S.P., Jeunen G.-J., Gemmell N.J. and Digby A. 2023. Non-invasive real-time genomic monitoring of the critically endangered kākāpō. eLife, 12: RP84553. https://doi.org/10.7554/eLife.84553.2

Ushio M., Murakami H., Masuda R., Sado T., Miya M., Sakurai S., Yamanaka H., Minamoto T. and Kondoh M. 2018a. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics, 2: e23297. https://doi.org/10.3897/mbmg.2.23297

Ushio M., Murata K., Sado T., Nishiumi I., Takeshita M., Iwasaki W. and Miya M. 2018b. Demonstration of the potential of environmental DNA as a tool for the detection of avian species. Scientific Reports, 8(1): 4493. https://doi.org/10.1038/s41598-018-22817-5

Valsecchi E., Bylemans J., Goodman S.J., Lombardi R., Carr I., Castellano L., Galimberti A. and Galli P. 2020. Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4): 460–476.https://doi.org/10.1002/edn3.72

Villacorta-Rath C., Hoskin C.J., Strugnell J.M. and Burrows D. 2021. Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations. PeerJ, 9: e12013. https://doi.org/10.7717/peerj.12013

Walker F.M., Sanchez D.E., Froehlich E.M., Federman E.L., Lyman J.A., Owens M. and Lear K. 2022. Endangered nectar-feeding bat detected by environmental DNA on flowers. Animals, 12: 3075. https://doi.org/10.3390/ani12223075

Wang Z., Liu X., Liang D., Wang Q., Zhang L. and Zhang P. 2023. VertU: universal multilocus primer sets for eDNA metabarcoding of vertebrate diversity, evaluated by both artificial and natural cases. Frontiers in Ecology and Evolution, 11: 1164206. https://doi.org/10.3389/fevo.2023.1164206

Xu C.C., Yen I.J., Bowman D. and Turner C.R. 2015. Spider web DNA: a new spin on noninvasive genetics of predator and prey. PloS one, 10(11): e0142503. https://doi.org/10.1371/journal.pone.0142503

Yamamoto S., Masuda R., Sato Y., Sado T., Araki H., Kondoh M., Minamoto T. and Miya M. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports, 7: 40368. https://doi.org/10.1038/srep40368

Yang S., Francis R.J., Holding M. and Kingsford R.T. 2024. Aerial photography and machine learning for estimating extremely high flamingo numbers on the Makgadikgadi Pans, Botswana. Global Ecology and Conservation, 53: e03011. https://doi.org/10.1016/j.gecco.2024.e03011

 

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