rarestR: An R Package Using Rarefaction Metrics to Estimate α‐ and β‐Diversity for Incomplete Samples

Diversity and Distributions, Journal Year: 2025, Volume and Issue: 31(1)

Published: Jan. 1, 2025

ABSTRACT Aim Species abundance data is commonly used to study biodiversity patterns. In this context, comparing α‐ and β‐diversity across incomplete samples can lead biases. Therefore, it essential employ methods that enable standardised accurate comparisons of varying sample sizes. addition, studies also often require robust estimates the total number species within a community shared by two communities. Innovation Rarefaction are calculate α‐diversity for sizes, they serve as basis calculating β‐diversity. application note, we present rarestR , new R package designed abundance‐based measures inconsistent using rarefaction‐based metrics. The includes parametric extrapolation techniques estimate expected community, well between Additionally, provides visualisation tools curve‐fitting associated with these estimators. Main Conclusions Overall, valuable tool values among samples, such those involving highly mobile or species‐rich taxa. our estimators offer complementary approach non‐parametric methods, including Chao series

Language: Английский

CEPHALOPOD, a package to standardize marine habitat‐modelling practices and enhance inter‐comparability across biological observations

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: May 7, 2025

Abstract As the volume of accessible marine pelagic observations increases exponentially, incorporating diverse data types such as metagenomics and quantitative imaging, need for standardized modelling frameworks becomes critical to predict biogeographic patterns in space time across range emergent sampling methods. In response, we introduce CEPHALOPOD (Comprehensive Ensemble Pipeline Habitat Across Large‐scale Ocean Pelagic Observation Datasets), a standardized, highly automated flexible framework designed integrate analyse heterogeneous multi‐species habitat following best practices field. is built on observational from federating initiatives AtlantECO, OBIS, GBIF, associated with already existing statistical machine learning methods that enable extract model information heterogeneous, scarce biased field observations. It follows explicit quality checks informing user predictive accuracy interpretability results. Here, document our ensemble approach then assess its strengths limitations virtual ecologist approach. We show how performs reproducing distributions samples. Our serves foundation consistent generation Essential Biodiversity Variables (EBVs EOVs) carries potential significantly advance comprehension biodiversity ecosystem functioning. Finally, it provides an unprecedented opportunity foster collaborations science, sustainable ecological practices, ultimately contribute preservation global biodiversity.

Language: Английский

Does the abiotic environment influence the distribution of flower and fruit colors?

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: May 14, 2025

Abstract Premise Color in flowers and fruits carries multiple functions, from attracting animal partners (pollinators, dispersers) to mitigating environmental stress (cold, drought, UV‐B). With research historically focusing on biotic interactions as selective agents, however, it remains unclear whether abiotic stressors impact flower fruit colors across large spatial scales shape their global distribution. Moreover, although are developmentally linked exposed the same macroclimatic conditions, they have similar (correlated) responses unknown. Methods Leveraging a data set of 2815 animal‐pollinated animal‐dispersed species 51 plant clades, we tested diversity distribution (scored into eight categories) is shaped by temperature, aridity, UV‐B irradiance. Results Global was uncoupled, with color generally lower than peaking areas high stress. Fruit peaked tropical where mutualists highest. These distinct patterns were different individual (for flowers, pink red cold temperatures, yellow purple irradiance; for fruits, wet black warm, yellow, green, orange Conclusions Our results challenge paradigm that primarily but instead indicate factors may macroecological stage evolution, acting fruits.

Language: Английский