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

Conservation of rare and cryptic species: Challenges of uncertainty and opportunities for progress DOI Creative Commons
Marie E. Martin, Matthew S. Delheimer, Katie M. Moriarty

et al.

Conservation Science and Practice, Journal Year: 2022, Volume and Issue: 4(11)

Published: Oct. 6, 2022

Abstract Effective conservation of at‐risk species presents a conundrum, often requiring rapid status assessments and timely actions regardless the adequacy best available information. Here, we present case study on Humboldt martens ( Martes caurina humboldtensis ), rare cryptic carnivore listed as threatened in 2020 under United States Endangered Species Act. Given their rarity, many aspects marten population ecology remain understudied. To help inform conservation, conducted exploratory analyses to estimate growth by incorporating empirically derived data into two demographic modeling approaches. Population rates from each approach exhibited substantial variability were uninformative evaluating status. Our results highlight inherent difficulties studying animals exemplify issues using sparse or uncertain potentially consequential circumstances. Considering shortcomings our findings, provide framework reliable improve future outcomes for poorly‐understood species.

Language: Английский

Citations

15

Taxonomic practice, creativity and fashion: what’s in a spider name? DOI Creative Commons
Stefano Mammola, Nathan Viel, Dylan Amiar

et al.

Zoological Journal of the Linnean Society, Journal Year: 2023, Volume and Issue: 198(2), P. 494 - 508

Published: Feb. 13, 2023

Abstract There is a secret pleasure in naming new species. Besides traditional etymologies recalling the sampling locality, habitat or morphology of species, names may be tributes to some meaningful person, pop culture references and even exercises enigmatography. Using dataset 48 464 spider etymologies, we tested hypothesis that species given by taxonomists are deeply influenced their cultural background. Specifically, asked whether practices change through space have changed time. In absolute terms, referring were most frequently used. relative peaked 1850–1900 then began decline, with parallel increase dedicated people geography. We also observed dramatic other aspects 2000–2020, especially Europe Americas. While such fashionable often carry no biological information regarding itself, they help give visibility taxonomy, discipline currently facing profound crisis academia. Taxonomy among unchanged disciplines across last centuries terms tools, rules writing style. Yet, our analysis suggests remain living time space.

Language: Английский

Citations

9

Passive acoustic monitoring and convolutional neural networks facilitate high-resolution and broadscale monitoring of a threatened species DOI Creative Commons
Adam Duarte, Matthew J. Weldy, Damon B. Lesmeister

et al.

Ecological Indicators, Journal Year: 2024, Volume and Issue: 162, P. 112016 - 112016

Published: April 13, 2024

Population monitoring is an essential component of biodiversity conservation and management, but low detection probabilities for rare and/or cryptic species makes estimating abundance occupancy challenging. Passive acoustic combined with machine learning algorithms represents a potential path forward to effectively efficiently monitor the occurrence vocalizing across entire forest landscapes. Our objectives were develop implement convolutional neural network (PNW-Cnet) identify vocalizations threatened nesting bird – marbled murrelet (Brachyramphus marmoratus) in Pacific Northwest, U.S.A., 2018–2021. We used PNW-Cnet predictions from broadscale passive data examine spatiotemporal patterns distribution murrelets. showed sufficiently high prediction accuracy (overall precision > 0.9) enable population monitoring. Spatiotemporal analysis that annual peak call occurs ordinal weeks 28–32 (late July–Mid August) this varied by study area. The greatest number detections typically occurred Olympic Peninsula Oregon Coast Range where late-successional dominates nearer ocean habitats. demonstrate can be understand intensity use broad scales addition typical detection/non-detection are often collected. offers considerable promise modeling long-term species.

Language: Английский

Citations

3

Functional Responses Shape Node and Network Level Properties of a Simplified Boreal Food Web DOI Creative Commons
Jenilee Gobin, Thomas J. Hossie, Rachael Derbyshire

et al.

Frontiers in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 10

Published: May 20, 2022

Ecological communities are fundamentally connected through a network of trophic interactions that often complex and difficult to model. Substantial variation exists in the nature magnitude these across various predators prey time. However, empirical data needed characterize relationships obtain natural systems, even for relatively simple food webs. Consequently, prey-dependent specifically hyperbolic form (Holling’s Type II), which consumption increases with density but ultimately becomes saturated or limited by time spent handling prey, most widely used albeit without knowledge their appropriateness. Here, we investigate sensitivity simplified web model natural, boreal system Kluane region Yukon, Canada type functional response used. Intensive study this community has permitted best-fit be determined, comprise linear (type I), sigmoidal III), prey- ratio-dependent relationships, inverse where kill rates alternate driven densities focal prey. We compare node- network-level properties interaction strengths estimated using responses one exclusively responses. show alone fail capture important ecological such as switching, surplus killing caching, predator interference, turn affect estimates cumulative rates, vulnerability generality predators, connectance. Exclusive use also affected trends observed metrics over underestimated annual several metrics, is given typically short periods. Our findings highlight need more comprehensive research aimed at characterizing when modeling predator-prey structure function, work toward mechanistic understanding linking dynamics systems.

Language: Английский

Citations

8

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

Citations

8