Ecology

Learn to analyse Ecological data through Galaxy.

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses

Material

Data and Metadata Management

These tutorials are focusing on data and metadata management in Ecology.

Data access

These lessons focus on ways to access data classicaly used in Ecology

Data preprocessing

These lessons focus on manners to preprocess data used in Ecology

Data analysis

These lessons focus on ways to analyse data in Ecology

Data visualization

These tutorials showcase data visualization in Ecology

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

Yvan Le Bras

Contributors

This material was contributed to by:

Yvan Le Bras

Pauline Seguineau

Glinez Thibaud

Marie Josse

Helena Rasche

Frédéric Boyer

Bérénice Batut

Ankerl Yassine

Eric Coissac

Dominique Pelletier

Tanguy Genthon

Jean-Baptiste Mihoub

Clara Urfer

Coline Royaux

Anne Fouilloux

Olivier Norvez

Soumya Jha

Brigida Gallone

Elisa Michon

Simon Benateau

Miguel Roncoroni

Clea Siguret

Funding

These individuals or organisations provided funding support for the development of this resource

EuroScienceGateway

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

ABRomics

PNDB

FNSO

This project (AAPFNSO2019OpenMetaPaper-14026) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.

Fair-Ease

FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.

References

• Reto Schmucki et al: A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes
  The rapid expansion of systematic monitoring schemes necessitates robust methods to reliably assess species' status and trends. Insect monitoring poses a challenge where there are strong seasonal patterns, requiring repeated counts to reliably assess abundance. Butterfly monitoring schemes (BMSs) operate in an increasing number of countries with broadly the same methodology, yet they differ in their observation frequency and in the methods used to compute annual abundance indices. Using simulated and observed data, we performed an extensive comparison of two approaches used to derive abundance indices from count data collected via BMS, under a range of sampling frequencies. Linear interpolation is most commonly used to estimate abundance indices from seasonal count series. A second method, hereafter the regional generalized additive model (GAM), fits a GAM to repeated counts within sites across a climatic region. For the two methods, we estimated bias in abundance indices and the statistical power for detecting trends, given different proportions of missing counts. We also compared the accuracy of trend estimates using systematically degraded observed counts of the Gatekeeper Pyronia tithonus (Linnaeus 1767). The regional GAM method generally outperforms the linear interpolation method. When the proportion of missing counts increased beyond 50%, indices derived via the linear interpolation method showed substantially higher estimation error as well as clear biases, in comparison to the regional GAM method. The regional GAM method also showed higher power to detect trends when the proportion of missing counts was substantial. Synthesis and applications. Monitoring offers invaluable data to support conservation policy and management, but requires robust analysis approaches and guidance for new and expanding schemes. Based on our findings, we recommend the regional generalized additive model approach when conducting integrative analyses across schemes, or when analysing scheme data with reduced sampling efforts. This method enables existing schemes to be expanded or new schemes to be developed with reduced within‐year sampling frequency, as well as affording options to adapt protocols to more efficiently assess species status and trends across large geographical scales.
• Vitor H. F. Gomes et al: Species Distribution Modelling: Contrasting presence-only models with plot abundance data
  Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model using inverse distance weighting (IDW)