Calculating functional diversity metrics using neighbor-joining trees DOI Creative Commons
Pedro Cardoso, Thomas Guillerme, Stefano Mammola

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 27, 2022

Abstract The study of functional diversity (FD) provides ways to understand phenomena as complex community assembly or the dynamics biodiversity change under multiple pressures. Different frameworks are used quantify FD, either based on dissimilarity matrices (e.g., Rao entropy, dendrograms) multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes). While first does not enable measurement FD within a richness/divergence/regularity framework, results in distortion space, latter allow for comparisons with phylogenetic (PD) measures and can be extremely sensitive outliers. We propose use neighbor-joining trees (NJ) represent way that combines strengths current without many their weaknesses. Our proposal is also uniquely suited studies compare PD, both share (NJ others) same mathematical principles. test ability this novel framework initial distances between species minimal space sensitivity using NJ compared conventional dendrograms, hypervolumes simulated empirical datasets. Using we demonstrate it possible combine much flexibility provided by simplicity tree-based representations. Moreover, method directly comparable PD measures, enables quantification richness, divergence regularity space.

Language: Английский

Emerging technologies revolutionise insect ecology and monitoring DOI Creative Commons
Roel van Klink, Tom August, Yves Bas

et al.

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

Citations

179

A protocol for reproducible functional diversity analyses DOI Creative Commons
Facundo X. Palacio, Corey T. Callaghan, Pedro Cardoso

et al.

Ecography, Journal Year: 2022, Volume and Issue: 2022(11)

Published: Aug. 30, 2022

The widespread use of species traits in basic and applied ecology, conservation biogeography has led to an exponential increase functional diversity analyses, with > 10 000 papers published 2010–2020, 1800 only 2021. This interest is reflected the development a multitude theoretical methodological frameworks for calculating diversity, making it challenging navigate myriads options report detailed accounts trait‐based analyses. Therefore, discipline ecology would benefit from existence general guideline standard reporting good practices We devise eight‐step protocol guide researchers conducting overarching goal increasing reproducibility, transparency comparability across studies. based on: 1) identification research question; 2) sampling scheme study design; 3–4) assemblage data matrices; 5) exploration preprocessing; 6) computation; 7) model fitting, evaluation interpretation; 8) data, metadata code provision. Throughout protocol, we provide information on how best select questions, designs, trait compute interpret results discuss ways ensure reproducibility results. To facilitate implementation this template, further develop interactive web‐based application ( stepFD ) form checklist workflow, detailing all steps allowing user produce final ‘reproducibility report' upload alongside paper. A thorough transparent analyses ensures that ecologists can incorporate others' findings into meta‐analyses, shared be integrated larger databases consensus available reused by other researchers. All these elements are key pushing forward vibrant fast‐growing field research.

Language: Английский

Citations

48

Novel community data in ecology-properties and prospects DOI
Florian Härtig, Nerea Abrego, Alex Bush

et al.

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

Published: Nov. 8, 2023

Language: Английский

Citations

38

Calculating functional diversity metrics using neighbor‐joining trees DOI Creative Commons
Pedro Cardoso, Thomas Guillerme,

Stefano Mammola

et al.

Ecography, Journal Year: 2024, Volume and Issue: 2024(7)

Published: April 30, 2024

The study of functional diversity (FD) provides ways to understand phenomena as complex community assembly or the dynamics biodiversity change under multiple pressures. Different frameworks are used quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, dendrograms) multidimensional spaces convex hulls, kernel‐density hypervolumes), each with their own strengths and limits. Frameworks do not enable measurement all components FD (i.e. richness, divergence, regularity), result in distortion space. allow for comparisons phylogenetic (PD) measures can be sensitive outliers. We propose use neighbor‐joining trees (NJ) represent a way that combines current without many weaknesses. Importantly, our approach is uniquely suited studies compare PD, both share (NJ others) same mathematical principles. test ability this novel framework initial distances between species minimal space sensitivity results using NJ compared conventional dendrograms, hypervolumes simulated empirical datasets. Using NJ, we demonstrate it possible combine much flexibility provided by simplicity tree‐based representations. Moreover, method directly comparable taxonomic (TD) PD measures, enables quantification divergence regularity

Language: Английский

Citations

10

Too much and not enough data: Challenges and solutions for generating information in freshwater research and monitoring DOI Creative Commons
Adrianne P. Smits, Ed K. Hall, Bridget R. Deemer

et al.

Ecosphere, Journal Year: 2025, Volume and Issue: 16(3)

Published: March 1, 2025

Abstract Evaluating progress toward achieving freshwater conservation and sustainability goals requires transforming diverse types of data into useful information for scientists, managers, other interest groups. Despite substantial increases in the volume collected worldwide, many regions ecosystems still lack sufficient collection and/or access. We illustrate how these challenges result from a set underlying mechanisms propose solutions that can be applied by individuals or organizations. discuss creative approaches to address scarcity, including use community science, remote‐sensing, environmental sensors, legacy datasets. highlight importance coordinated efforts among groups training programs improve At institutional level, we emphasize power prioritizing curation, incentivizing publication, promoting research enhances coverage representativeness. Some strategies involve technological analytical approaches, but necessitate shifting priorities incentives organizations such as academic government institutions, monitoring groups, journals, funding agencies. Our overarching goal is stimulate discussion narrow disparities hindering understanding processes their change across spatial scales.

Language: Английский

Citations

1

The digital peregrine: A technonatural history of a cosmopolitan raptor DOI Creative Commons
Adam Searle, Jonathon Turnbull, William M. Adams

et al.

Transactions of the Institute of British Geographers, Journal Year: 2022, Volume and Issue: 48(1), P. 195 - 212

Published: Aug. 15, 2022

Abstract Humans, non‐human animals, and technologies are increasingly entangled. Using the peregrine falcon ( Falco peregrinus ) as an illustrative example, we propose ‘technonatural history’ a theoretical methodological approach for observing, describing, examining role play in shaping human relations with other species. After nearing extinction 20th century, peregrines have become woven into fabric of everyday urban life frequently sighted raptor UK, nesting on high‐rise buildings church spires since late 1990s. Their unexpected presence cities symbolises hope multispecies conviviality amid contemporary ecological crisis. As their populations resurged, crucially, webcam livestreaming developed rapidly. Peregrines were one first animals to be broadcast over internet via ‘nestcams’, granting broad publics access intimate lives. We examine related technological histories natural falcons tracing emergence ‘the digital peregrine’ its manifold implications more‐than‐human geographies. To do so, build oral history interviews people associated throughout UK: nestcam technicians, conservationists, professional ecologists, activists, citizen scientists. While digitisation brings closer these cosmopolitan raptors, they can only ever grasp at wildness wider milieus is distinct entity, encountered own set affects affordances. In peregrine's case, create radical opportunities conviviality, signalling positive potentials host forging meaningful connections.

Language: Английский

Citations

29

How much biodiversity is concealed in the word ‘biodiversity’? DOI Creative Commons
Stefano Mammola, Caroline Sayuri Fukushima,

Girolama Biondo

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(2), P. R59 - R60

Published: Jan. 1, 2023

Amidst a global biodiversity crisis1, the word 'biodiversity' has become indispensable for conservation and management2. Yet, is often used as buzzword in scientific literature. Resonant titles of papers claiming to have studied 'global biodiversity' may be promote research focused on few taxonomic groups, habitats, or facets - taxonomic, (phylo)genetic, functional. This usage lead extrapolating results outside target systems these studies with direct consequences our understanding life Earth its practical conservation. Here, we random sample their title take long view use this term. Despite improvements analytical tools, monitoring technologies, data availability3,4, found that scope articles not increased recent years. We also show wider attract more citations online attention. Our broad ramifications how from narrow affects

Language: Английский

Citations

21

The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education DOI Creative Commons
Karma Nanglu, Danielle de Carle, Thomas M. Cullen

et al.

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(10)

Published: Oct. 1, 2023

There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education favor theoretical, laboratory, or simulation-based programs. This may take form removing biodiversity and field courses from curriculum sometimes subtle maligning as "lesser" branch science. Additional threats include massive funding cuts museums maintenance their collections, extirpation taxonomists across disciplines, critical under-appreciation role that data (and other forms observational data, including Indigenous knowledge) play scientific process. In this paper, we demonstrate knowledge integral any competitive science program through comprehensive review ways which they continue shape modern theory public perception We do so by reviewing how has guided disciplines ecology, evolution, conservation are crucial for effective programs policy. underscore these insights with case studies, including: understanding dynamics evolutionary radiation relies on data; methods extracting novel museum specimens; provided multi-decade programs; most logical venue creating an informed scientifically literate society. conclude recommendations aimed at students, university faculty, administrators integrating supporting mandates. Fundamentally, all interested world, but can often fall into habit abstracting our away its contexts complexities. Doing risks losing sight entire vistas new questions over-emphasis simulated overly controlled studies.

Language: Английский

Citations

21

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity DOI Creative Commons
Yuanheng Li, Christian Devenish, Marie I. Tosa

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier study, since can be mass-trapped, mass-identified, and semi-mass-quantified into ‘many-row (observation), many-column (species)‘ datasets, with homogeneous error, high resolution, copious environmental-covariate information. These ‘novel community datasets’ let us efficiently generate information on arthropod species distributions, values, uncertainty, magnitude direction human impacts. We use a DNA-based method (barcode mapping) produce an arthropod-community dataset from 121 Malaise-trap samples, combine it 29 remote-imagery layers using deep neural net in joint distribution model. With this approach, we maps for 76 across 225 km 2 temperate-zone forested landscape. visualize fine-scale spatial distributions richness, composition, site irreplaceability. Old-growth forests show distinct composition higher stream courses have highest site-irreplaceability values. ‘sideways biodiversity modelling’ method, demonstrate feasibility mapping at sufficient resolution inform local management choices, while also being efficient enough scale up thousands square kilometres. article is part theme issue ‘Towards toolkit global insect monitoring’.

Language: Английский

Citations

5

Using passive acoustic monitoring to estimate northern spotted owl landscape use and pair occupancy DOI Creative Commons
Cara L. Appel, Damon B. Lesmeister, Adam Duarte

et al.

Ecosphere, Journal Year: 2023, Volume and Issue: 14(2)

Published: Feb. 1, 2023

Abstract Managing forests for biodiversity conservation while maintaining economic output is a major challenge globally and requires accurate timely monitoring of imperiled species. In the Pacific Northwest, USA, forest management heavily influenced by status northern spotted owls ( Strix occidentalis caurina ), which have been in continued population decline past four decades. The program transitioning from mark–resight surveys to passive acoustic framework, requiring development alternative analysis approaches. To maintain relevance management, these analyses must accurately track underlying changes, identify responses disturbance, estimate occupancy owl pairs. We randomly selected surveyed 5‐km 2 hexagons 6 weeks using Olympic Peninsula Washington Oregon Coast Range during 2018 breeding season. used convolutional neural network calls, followed logistic regression determine sex vocalizing assign pair status. implemented multistate models probabilities detection, species‐level landscape use, owls. also quantified detections barred varia congeneric competitor important driver declines. overall rate hexagon use was estimated at 0.21 (SD 0.04) after adjusting imperfect 0.07 0.02). probability detecting (i.e., both female male) weekly occasion relatively low (0.03, SD 0.01), indicating that true between 1.3 4.1 times greater than proportion with observed detections. Barred were ubiquitous, naïve 0.97. intensity calling had weak, negative effect on being paired when present but little measurable their detectability. This work establishes framework may be effective illustrates pairs very detection probability, which—combined increasingly numbers pairs—is an consideration management.

Language: Английский

Citations

11