DOI: 10.5061/dryad.9ghx3ffv5
title: Shade coffee agroforests as native plant sources for restoration

description: 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.
description: # Shade coffee agroforests as native plant sources for restoration Dataset
 DOI: [10.5061/dryad.9ghx3ffv5](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 (&gt;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&lt;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.