Shade coffee agroforests as native plant sources for restoration
Data files
Mar 27, 2025 version files 307.75 KB
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Osuri_et_al_native_trees_r1.zip
300.97 KB
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README.md
6.77 KB
Abstract
Tropical agroforestry systems such as shade coffee are recognised as important refuges for biodiversity in human-modified landscapes. In these systems, many conservation initiatives aiming to sustain biodiversity against the trend of intensifying agroforestry management focus on promoting biodiverse tree overstories, but engage less with conservation opportunities and challenges associated with agroforest understories. In coffee agroforests with native shade trees, weeding of natural regeneration constitutes lost conservation opportunities. We explore the potential for reducing such losses by rescuing native tree seeds and naturally regenerating seedlings from coffee agroforests and developing local native plant nurseries, which are a critical bottleneck for restoration. For this, we draw on floristic surveys using 42 0.3 ha plots in eight polyculture shade coffee agroforests and collaborative pilot rescue, nursery development, and restoration initiatives in the Western Ghats biodiversity hotspot, India. Ninety restoration-relevant native tree species (inferred from species distributions, traits, and practitioner knowledge) constituted 37% of all trees recorded in coffee agroforests. The species list included 30 conservation-priority species (endemic to the Western Ghats and/or classified as threatened or near-threatened by the IUCN), most of which were not stocked in existing public nurseries. Experiences from pilot rescue efforts, which collected over 18,000 seeds and seedlings spanning 56 restoration-relevant species in 12 months, underscore the importance of efficient rescue planning focussed on mapping target trees and monitoring phenology, fostering partnerships with agroforest landowners to enhance rescue opportunities, and developing nursery infrastructure to house rescued plants and support local restoration efforts.
Synthesis and applications: Shade coffee agroforests can contribute to conservation beyond their boundaries as sources of native plants that can help expand and diversify local nurseries and scale up restoration, while alleviating the need to exploit remnant natural forests as plant sources for nurseries and restoration. Harnessing this opportunity requires the development of strategies and partnerships for integrating native plant sourcing, nursery, and restoration efforts, backed by policies and initiatives that promote landscape-level benefits of agroforestry for biodiversity and conservation.
Dataset DOI: 10.5061/dryad.9ghx3ffv5
Description of the data and file structure
This document describes the dataset used in Osuri et al.(2025) Shade coffee agroforests as native plant sources for restoration.
Files and variables
File: Osuri_et_al_native_trees.zip
Description: This document describes the dataset used in Osuri et al.(2025) Shade coffee agroforests as native plant sources for restoration.
The contents of the .xlsx data file are described below:
File name:”Osuri_et_al_native_trees.xlsx”
—–Sheet 1: “adult_trees.xlsx”—–
Description: This sheet contains the diameter at breast height (dbh), height and species identity of all the trees with a diameter above 10 cm in 150m x 20m vegetation plots in shade coffee agroforests. Trees that could not be identified to the species level are recorded using their genus name alone, and unidentified trees are labelled UID.
Column names and descriptions:
sno.: A unique identifier for each row in the dataset.
plantationname: Name of the sampled shade coffee agroforest.
transectid: A unique identifier for vegetation transects.
category: Classifies the sampled agroforest based on annual rainfall as either wet (>2800 mm) or dry (2000-2800 mm)
type: Specifies whether the sampled transect was established in a Coffea arabica or Coffea canephora agroforest.
treeid: Tree species scientific name (standardised with reference to Plants of the World Online)
treeheight: The height of the tree (m). NA if not measured.
treedbh1-7: Diameter at breast height (DBH) of the tree (cm). If the tree had multiple stems at breast height, their individual diameters were measured and recorded in the subsequent columns. In the case of single-stemmed trees, the rows treedbh1 to treedbh7 are assigned NA.
notes: General remarks about the transects and trees.
—–Sheet 2: “juvenile_density.xlsx”—–
Description: This sheet contains counts of juvenile trees (dbh<10 cm) recorded in the four 5m x 5m plots nested within 150m X 20m plots in shade coffee agroforests.
Column names and descriptions:
sno.: A unique identifier for each row in the dataset.
treeid: Tree species scientific name (standardised with reference to Plants of the World Online); NAs entered in case no trees were recorded in the subplot
count : Number of individuals recorded of a species in a plot; NAs entered in case no trees were recorded in the subplot
plot.interval : Unique identifier for each 5m x 5m plot on the vegetation transects.
transectid : A unique identifier for vegetation transects.
plot.area : Area of the plot (ha).
type: Specifies whether the sampled transect was established in a Coffea arabica or Coffea canephora (Robusta) plantation.
plantation : Shade coffee agroforest name.
remarks: General remarks about the transect and the plot.
weeding.frequency: Whether the sampled estates are frequently weeded, infrequently weeded, or have not been weeded over the five years preceding the study.
—–Sheet 3: “juvenile_diversity.xlsx”—–
Description: This sheet contains records of the presence of tree species as juveniles in 150m X 20m vegetation plots in shade coffee agroforests.
Column names and descriptions:
sno.: Unique identifier for each row.
treeid: Tree species scientific name (standardised with reference to Plants of the World Online)
seedling.genus : Genus of the juvenile species.
seedling.family : Family to which the juvenile species belongs to.
transectid : A unique identifier for vegetation transects.
type: Specifies whether the sampled transect was established in a Coffea arabica or Coffea canephora (Robusta) agroforest.
plantation : Shade coffee agroforest name.
remarks: General remarks about the transect and the plot.
weeding.frequency: : Whether the sampled estates are frequently weeded, infrequently weeded, or have not been weeded over the five years preceding the study.
—–Sheet 4: “species_traits.xlsx”—–
Description: This sheet contains trait data all tree species recorded in this study.
Column names and descriptions:
treeid: Tree species scientific name (standardised with reference to Plants of the World Online)
habit: Specifies whether the species is a tree or a shrub.
successional status: The tropical forest successional stage to which the species is most closely affiliated. Species that do not fit within these categories are classified as “other.” “NA” if unknown.
relevance for restoration: Species relevance for restoration, assessed based on geographic range and practitioner knowledge. “NA” if unknown.
origin: Indicates the species’ biogeographical classification—whether it is endemic to the Western Ghats, a native evergreen species, a native species found in other forest types, or an introduced species. “NA” if unknown.
iucn status: Specifies the conservation status of the species based on the IUCN Red List categories: Extinct, Extinct in the Wild, Critically Endangered, Endangered, Vulnerable, Near Threatened, Least Concern, Data Deficient, or Not Evaluated. “NA” if unknown.
disperser: Identifies whether the species is dispersed by animals (biotic dispersal) or through abiotic mechanisms. “NA” if unknown.
—–Sheet 5: “rescued_seeds_wildlings.xlsx”—–
Description: This sheet contains the species list and counts of seeds and wildlings rescued from the shade coffee agroforests during the project period.
Column names and descriptions:
sno.: Unique identifier for each row.
treeid: Tree species scientific name (standardised with reference to Plants of the World Online)
number of seeds collected : Count of seeds of different species collected from shade coffee agroforests.
number of seedlings collected : Count of wildlings of different species collected from shade coffee agroforests.
—–Sheet 6: “public_nursery_seedling_species.xlsx”—–
Description: This sheet contains the list of species recorded in public nurseries operated by the State forest department in the project landscape.
Column names and descriptions:
sno.: Unique identifier for each row.
treeid: Tree species scientific name (standardised with reference to Plants of the World Online)
—–Sheet 7: “site_locations.xlsx”—–
Description: This sheet contains the coordinates of the sampled plots at the shade coffee agroforests.
Column names and descriptions:
sno.: Unique identifier for each row.
transectid: A unique identifier for vegetation transects.
lat: specifies the latitude of the plot centroid (degree decimal).
Long: specifies the east-west position of the plot centroid.
Code/software
An R script is included.