How genomics can help biodiversity conservation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

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Emerging technologies revolutionise insect ecology and monitoring

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(10), P. 872 - 885

Published: July 8, 2022

Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances potential revolutionise insect ecology monitoring. We describe state art four technologies (computer vision, acoustic monitoring, radar, molecular methods), assess advantages, current limitations, future potential. discuss how these can adhere modern standards data curation transparency, implications for citizen science, integration among different monitoring programmes technologies. argue that they provide unprecedented possibilities it will be important foster international via collaboration.

Language: Английский

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Airborne environmental DNA for terrestrial vertebrate community monitoring

Current Biology, Journal Year: 2022, Volume and Issue: 32(3), P. 701 - 707.e5

Published: Jan. 6, 2022

Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, movements, it key to understanding tracking environmental anthropogenic effects on natural ecosystems.1Navarro L.M. Fernández N. Guerra C. Guralnick R. Kissling W.D. Londoño M.C. Muller-Karger F. Turak E. Balvanera P. Costello M.J. et al.Monitoring biodiversity change through effective global coordination.Curr. Opin. Environ. Sustain. 2017; 29: 158-169Crossref Scopus (89) Google Scholar, 2Xu H. Cao Y. Yu D. M. He Gill Pereira H.M. Ensuring implementation post-2020 targets.Nat. Ecol. Evol. 2021; 5: 411-418Crossref PubMed (30) 3(2021). High time invest in biodiversity. Nat. 5, 263.Google 4Seibold S. Gossner M.M. Simons N.K. Blüthgen Müller J. Ambarli al.Arthropod decline grasslands forests associated with landscape-level drivers.Nature. 2019; 574: 671-674Crossref (391) Scholar Vertebrates terrestrial ecosystems are experiencing extinctions declines both population numbers sizes due increasing threats from human activities change.5Almond R.E.A. Grooten Petersen T. Living Planet Report 2020: Bending Curve Loss. WWF, 2020Google 6Ceballos G. Ehrlich P.R. Dirzo Biological annihilation via ongoing sixth mass extinction signaled by vertebrate losses declines.Proc. Natl. Acad. Sci. USA. 114: E6089-E6096Crossref (1031) 7Hughes J.B. Daily G.C. Population diversity: its extent extinction.Science. 1997; 278: 689-692Crossref (381) 8Gaston K.J. Fuller R.A. Commonness, depletion conservation biology.Trends 2008; 23: 14-19Abstract Full Text PDF (361) Terrestrial using existing methods generally costly laborious, although DNA (eDNA) becoming tool choice assess biodiversity, few sample types effectively capture diversity. We hypothesized that eDNA captured air could allow straightforward collection characterization communities. filtered three localities Copenhagen Zoo: stable, outside between outdoor enclosures, Rainforest House. Through metabarcoding airborne eDNA, we detected 49 spanning 26 orders 37 families: 30 mammal, 13 bird, 4 fish, 1 amphibian, reptile species. These spanned animals kept zoo, occurring zoo surroundings, used as feed zoo. The comprise range taxonomic families, sizes, behaviors, abundances. found shorter distance sampling device higher animal biomass increase probability detection. hereby show can offer fundamentally new way

Language: Английский

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Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(20), P. 5132 - 5164

Published: Aug. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Language: Английский

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Novel community data in ecology-properties and prospects

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 39(3), P. 280 - 293

Published: Nov. 8, 2023

Language: Английский

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Freshwater fungal biology

Mycosphere, Journal Year: 2023, Volume and Issue: 14(1), P. 195 - 413

Published: Jan. 1, 2023

Research into freshwater fungi has generated a wealth of information over the past decades with various published articles, i.e., reviews, books, and monographs.With advancement methodologies used in fungal research, numerous mycologists working on this ecological group, our knowledge progress understanding fungi, including novel discoveries new insights ecology advanced.With enormous progress, it is timely that an updated account be compiled one volume.Thus, to give comprehensive overview different facets biology.It includes classification scheme based latest taxonomic phylogenetic analysis taxa, their evolutionary history.The biology, diversity, geographical distribution higher basal are also discussed entries.A section dispersal adaptation filamentous included present work.The importance role breakdown wood habitats, physiology, detail.The biotechnological potential as producers bioactive metabolites reviewed, antimicrobial drug discovery.The volume provides high throughput sequencing (HTS) platforms for research highlighting advantages challenges, recent studies HTS identification quantification communities habitats.The identifies gaps direction future fungi.

Language: Английский

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Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(3), P. 847 - 861

Published: Sept. 8, 2021

Metabarcoding of DNA extracted from community samples whole organisms (whole organism DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities provide rapid, accurate high resolution data for novel molecular ecology research. The growth this field has been accompanied by considerable development that builds on microbial metabarcoding methods develop appropriate efficient sampling laboratory protocols communities. However, considerably less attention focused ensuring bioinformatic are adapted comprehensively in wocDNA metabarcoding. In study we examined over 600 papers identified 111 studies performed COI wocDNA. We then systematically reviewed the employed these identify state-of-the-art. Our results show increasing use diversity characterised a clear absence harmonisation, temporal trends little change situation. literature showed (i) heterogeneity across pipelines, tasks tools used, (ii) limited or no adaptation procedures nature fragment, (iii) worrying underreporting tasks, software parameters. Based upon findings propose set recommendations think should consider ensure appropriate, comprehensive comparable. believe adhering will improve long-term integrative potential biodiversity science.

Language: Английский

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Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(2), P. e0289437 - e0289437

Published: Feb. 14, 2024

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in monitoring provides an opportunity improve practices. Approaches directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing site-specific community composition DNA (eDNA) can provide timely, relevant results for parties interested success agricultural To measured impacts due projects not exogenous factors, sites where have been implemented should be benchmarked against counterfactuals (no project) control (natural habitat) sites. Results then used calculate diverse sets indicators customized different projects. Here, we report on our experience developing applying one such approach assess impact shaded cocoa Instituto de Manejo e Certificação Florestal Agrícola (IMAFLORA) near São Félix do Xingu, Pará, Brazil. We Continuous Degradation Detection (CODED) LandTrendr algorithms create a sensing-based assessment forest disturbance regeneration, estimate carbon sequestration, changes habitats. coupled these methods with eDNA analyses using arthropod-targeted primers collecting soil samples intervention counterfactual pasture field secondary forest. custom set pilot application framework called TerraBio. Our suggest that, IMAFLORA’s projects, over 400 acres were restored area arthropods closer second-growth forests than pastures. In reviewing approach, found multiple aspects worked well, conclude presenting lessons learned.

Language: Английский

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Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond global change. However, large-scale syntheses may be compromised if workflows differ from each other. There are ongoing efforts improve standardization the reporting inventory harmonization at stage metabarcode has yet addressed. A modular framework harmonized generation a pathway navigate complex structure terrestrial metazoan biodiversity. Here, through our collective expertise practitioners, method developers, researchers leading initiatives we seek initiate generation, arthropod module. We develop initial set submodules covering 5 main steps generation: (i) sample acquisition; (ii) processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, sequencing; (v) sequence metadata deposition, providing backbone To achieve this, identified key points harmonization, reviewed current state art, distilled existing knowledge within submodules, thus promoting best practice by guidelines recommendations reduce universe methodological options. advocate adoption further development encourage modules other fractions step toward synthesis harmonization.

Language: Английский

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Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(5)

Published: May 1, 2022

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude species, which well defined complex shape male genitalia. Here, we how COI barcode data reflect morphological species entities thus their usability for accelerated inventorization. We conducted dedicated field surveys Sri Lanka collect species-rich highly endemic Sericini (Coleoptera: Scarabaeidae). Congruence among results series protocols de novo delimitation with morphology-based identifications was investigated. Different methods, such as Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species Partitioning (ASAP), Index Number (BIN) assignments, resulted different numbers molecular operational taxonomic units (MOTUs). All methods showed both over-splitting lumping morphologically identified species. Only 18 observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence between expressed match ratio low, ranging 0.57 0.67. TCS multirate PTP (mPTP) highest ratio, while assignment lowest splitting events. mPTP lumped more than any other method. Principal coordinate analysis (PCoA) on ratio-based distance matrix revealed incongruent outcomes multiple although applied same data. Our confirm that alone unlikely correctly delimit particular, when using only single approach. encourage integration various approaches data, particularly morphology, validate boundaries.

Language: Английский

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