Study sites and plot characteristics
DR Danaë M. A. Rozendaal  FB Frans Bongers TA T. Mitchell Aide EA Esteban Alvarez-Dávila NA Nataly Ascarrunz PB Patricia Balvanera JB Justin M. Becknell TB Tony V. Bentos PB Pedro H. S. Brancalion GC George A. L. Cabral SC Sofia Calvo-Rodriguez JC Jerome Chave RC Ricardo G. César RC Robin L. Chazdon RC Richard Condit JD Jorn S. Dallinga JA Jarcilene S. de Almeida-Cortez BJ Ben de Jong AO Alexandre de Oliveira JD Julie S. Denslow DD Daisy H. Dent SD Saara J. DeWalt JD Juan Manuel Dupuy SD Sandra M. Durán LD Loïc P. Dutrieux ME Mario M. Espírito-Santo MF María C. Fandino GF G. Wilson Fernandes BF Bryan Finegan HG Hernando García NG Noel Gonzalez VM Vanessa Granda Moser JH Jefferson S. Hall JH José Luis Hernández-Stefanoni SH Stephen Hubbell CJ Catarina C. Jakovac AH Alma Johanna Hernández AJ André B. Junqueira DK Deborah Kennard DL Denis Larpin SL Susan G. Letcher JL Juan-Carlos Licona EL Edwin Lebrija-Trejos EM Erika Marín-Spiotta MM Miguel Martínez-Ramos PM Paulo E. S. Massoca JM Jorge A. Meave RM Rita C. G. Mesquita FM Francisco Mora SM Sandra C. Müller RM Rodrigo Muñoz SN Silvio Nolasco de Oliveira Neto NN Natalia Norden YN Yule R. F. Nunes SO Susana Ochoa-Gaona EO Edgar Ortiz-Malavassi RO Rebecca Ostertag MP Marielos Peña-Claros EP Eduardo A. Pérez-García DP Daniel Piotto JP Jennifer S. Powers JA José Aguilar-Cano SR Susana Rodriguez-Buritica JR Jorge Rodríguez-Velázquez MR Marco Antonio Romero-Romero JR Jorge Ruíz AS Arturo Sanchez-Azofeifa AA Arlete Silva de Almeida WS Whendee L. Silver NS Naomi B. Schwartz WT William Wayt Thomas MT Marisol Toledo MU Maria Uriarte ES Everardo Valadares de Sá Sampaio MB Michiel van Breugel HW Hans van der Wal SM Sebastião Venâncio Martins MV Maria D. M. Veloso HV Hans F. M. Vester AV Alberto Vicentini IV Ima C. G. Vieira PV Pedro Villa GW G. Bruce Williamson KZ Kátia J. Zanini JZ Jess Zimmerman LP Lourens Poorter
This protocol is extracted from research article:
Biodiversity recovery of Neotropical secondary forests
Sci Adv, Mar 6, 2019; DOI: 10.1126/sciadv.aau3114

Chronosequence data were compiled for 56 Neotropical lowland forest sites, in 10 countries, covering the entire latitudinal gradient in the Neotropics (Fig. 1 and table S1) (15). To reduce the confounding effect of elevation, we included sites that were generally below 1000 m above sea level. Annual rainfall varied from 750 to 6000 mm across sites, topsoil CEC varied from 1.7 to 64.6 cmol(+) kg−1, and percentage of forest cover in the landscape matrix ranged from 9.4 to 99.9% (table S1).

We aimed to assess the rate and extent of biodiversity recovery after abandonment of pastures and shifting cultivation fields. Shifting cultivation is typically performed at a small scale, in which patches of 0.5 to 1 ha are slashed, burned, cultivated, or used as pasture for some years and abandoned, after which they recover (13, 14). We were therefore interested in recovery of alpha diversity at the scale of these local patches. To avoid edge effects of neighboring old-growth forest, secondary forest researchers typically establish small plots (0.1 ha; see below) in abandoned fields. For each chronosequence site, an average of 29.1 plots (range, 4 to 251) were included, with secondary forest plots ranging in stand age from 1 to 100 years across sites (table S1). Plot ages were estimated using landowner interviews (33 sites), satellite images or aerial photographs (6 sites), landowner interviews combined with tree-ring counts (1 site), and satellite images and/or aerial photographs that were combined with information from landowner interviews (16 sites). In general, age estimates for young secondary plots were regarded to be more precise (precise to the year or to 6 months for some sites) than age estimates for older secondary forest plots (error of a few years), and this is exactly what is needed given that initial recovery goes fast (thus exact age estimates are important) and that later in succession recovery rates slow down. Data from old-growth forests were included as a reference for estimating biodiversity recovery for 45 of the 56 sites (table S1). Old-growth forests had no record of previous disturbance for at least 100 years. Plot sizes ranged from 0.01 to 1 ha, with an average of 0.09 ha across all plots. To accurately estimate biodiversity recovery, we assured that, within each chronosequence site, secondary forest plots and old-growth plots had similar sizes, but for 12 sites, old-growth plots were slightly larger or smaller than secondary forest plots (table S1). All stems ≥5 cm dbh of trees, palms, and shrubs were measured for dbh and identified to species, with the exception of six sites for which the minimum dbh was 10 cm. Across chronosequences, on average, 92.8% of the stems were identified to species (range, 58 to 100%) and 99.6% (range, 94 to 100%) were identified to family, genus, species, or morphospecies (table S2).

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