DOI: 10.5061/dryad.kh18932ht
title: Data from: Partial recovery of primary rainforest bird communities in Amazonian secondary forests

description: Loss of primary rainforest imperils species, communities, and ecosystem
 services. Secondary forests play a role in supporting primary forest
 species, making it important to assess how variation in landscape
 composition, sample area, and secondary forest age influence their value
 for maintaining biodiversity. We sampled bird communities in three 16-ha
 sites in 31-36-year-old secondary forest (SF) and three adjacent primary
 forest (PF) sites at the Biological Dynamics of Forest Fragments Project
 near Manaus, Brazil. SF sites were surrounded by vast, minimally broken
 PF. Spot-map surveys revealed 204 species, with 48 found only in PF (SF
 estimate 117-144 species/site, PF estimate 163-180). SF communities were
 distinct, but composed almost entirely of PF species and overlapped PF
 communities in functional attributes. Cavity-nesting species were slightly
 underrepresented in SF. Important differences in SF included much reduced
 abundance of canopy, terrestrial, and insectivorous species. Vegetation
 structure may limit canopy species: SF had a homogeneous canopy of 20-25
 m, &gt;10m lower than the heterogeneous PF canopy. Sensitivity of
 terrestrial insectivores conforms to an expected pattern, perhaps
 exacerbated by a lack of colonists for these regionally declining species.
 Relatively better recovery of midstory and understory species does not
 align with some studies, perhaps because our landscape facilitated their
 colonization. In this system, SF bird communities appear to be recovering,
 with frugivores, nectarivores, and granivores (including game species)
 already well matched to PF. Complete recovery may be slowed not just by SF
 habitat suitability, but also by demographic processes in PF that limit
 availability of colonists.
description: Field data of bird spotmaps, with additional columns added for
 data from other sources.  See the metadata file.
description: # Partial Recovery of Primary Rainforest Bird Communities in
 [https://doi.org/10.5061/dryad.kh18932ht](https://doi.org/10.5061/dryad.kh18932ht) ## Description of the data and file structure **Description:** Spot-map dataset metadata followed by veg dataset metadata * **spot_map_data_final** ## Spot-map metadata ##### Variables Data collected in the field: | ID1 | | line code from Access | | :--------- | :- | :------------------------------------------------------------------------------------------------ | | species | | species code | | sp | | species name from our database- updated in the paper for current taxonomy | | dt | | m/d/y | | hr | | hh:mm | | sx | | 1=m, 2=f, 3= unknown | | | | | | SpCount | | number of individuals | | OBS | | how observed- 1=seen, 2=heard, 3=seen and heard | | HEARD | | vocalization if bird was not seen only- 0= seen only, 1=singing, 2=calling, 3=singing and calling | | OBSERVER | | CLR= Cameron Rutt, cv = Claudier Vargas, ps=Phil Stouffer | | INorOUT | | in or out of the plot- 1=in, 2= out | | LOCATION | | 1-ha subplot 1-16, or nearest subplot for birds outside the plot | | OVERFLIGHT | | flyover only- 1=flyover, 2= not flyover | | STATION | | plots 1-6 | Data added: Plot codes (third column corresponds to 'station' from original data: | P1 | 11 | 3 | | Porto Alegre continuous forest | | :- | :- | :- | :- | :-------------------------------------------------------------------- | | P2 | 12 | 5 | | Cabo Frio continuous forest to sw | | P3 | 13 | 6 | | Cabo Frio continuous forest within team plot | | S1 | 21 | 1 | | Porto Alegre 2nd growth plot to the north (nearest the 10ha fragment) | | S2 | 22 | 2 | | Porto Alegre 2nd growth plot near camp | | S3 | 23 | 4 | | Cabo Frio 2nd growth plot near LBA tower | Additional data: | visit | Replicate days of sampling- sample 1-11 at each site | | :------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | cavity | From Van der Hoek 2017, with corrections form Kristina Cockle. 0=not cavity nester, 1= cavity nester | | habitat  | From habitat code in Cohn-Haft et al. list, only indicated for birds that do not have 1 (primary forest) in the first position of the code. Species with no data have 1 (primary forest) as their primary habitat. | | stratum | Position/microhabitat (stratum) from Cohn-Haft et al. list | | guild | Diet from Johnson et al. or similar species if not on the list | Note- 8 observations of spuhs counted as observations but not species Plot coordinates | Plot coordinates | | | | | | | | | | :--------------- | :------ | :------- | :------ | :------- | :------ | :------- | :------ | -------- | | plot   | ne lat | ne long | nw lat | nw long | se lat | se long | sw lat | sw long | | P1 | -2.3740 | -59.9569 | -2.3747 | -59.9605 | -2.3779 | -59.9565 | -2.3781 | -59.9600 | | P2 | -2.3938 | -59.9005 | -2.3907 | -59.9015 | -2.3960 | -59.9025 | -2.3929 | -59.9043 | | P3 | -2.4044 | -59.8964 | -2.4031 | -59.9000 | -2.4078 | -59.8976 | -2.4063 | -59.9009 | | S1 | -2.3592 | -59.9637 | -2.3563 | -59.9659 | -2.3605 | -59.9671 | -2.3580 | -59.9692 | | S2 | -2.3724 | -59.9723 | -2.3705 | -59.9757 | -2.3756 | -59.9743 | -2.3736 | -59.9771 | | S3 | -2.3885 | -59.8833 | -2.3868 | -59.8865 | -2.3917 | -59.8848 | -2.3900 | -59.8880 | Subplot orientation | Subplot orientation (1,5,9,13 always along the same border, same with 4,8,12,16) | | | | | | :------------------------------------------------------------------------------- | -- | -- | -- | -- | | plot | ne | nw | se | sw | | P1 | 4 | 1 | 16 | 13 | | P2 | 16 | 13 | 1 | 4 | | P3 | 1 | 4 | 13 | 16 | | S1 | 16 | 4 | 13 | 1 | | S2 | 4 | 1 | 16 | 13 | | S3 | 4 | 1 | 16 | 13 | * **veg_data_final** ## Veg metadata Variables | Site | Same as in spot map spreadsheet-  | | | | | :--- | :-------------------------------- | :- | - | --------------------------------------------------------------------- | | P1 | 11 | 3 | | Porto Alegre continuous forest | | P2 | 12 | 5 | | Cabo Frio continuous forest where Cameron worked | | P3 | 13 | 6 | | Cabo Frio continuous forest within team plot | | S1 | 21 | 1 | | Porto Alegre 2nd growth plot to the north (nearest the 10ha fragment) | | S2 | 22 | 2 | | Porto Alegre 2nd growth plot near camp (where Cameron worked) | | S3 | 23 | 4 | | Cabo Frio 2nd growth plot near LBA tower | | Plot | Original plot names used in the field | | :----------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Location | Subplot 1-16 of the plot,  8 chosen at random with no repeats.  Each veg sample plot was 8m radius (201m2) | | CanopyHT1-4  | Canopy height (m, taken with a digital rangefinder by Cameron), from the middle of each of the four quadrants of the 8m radius plot (1-4 here and for veg presence) | | DBHmax | DBH (cm) of the largest tree on the 8 m radius plot | | Leaves 1-4 | Count of number of leaves in litter at canopy point 1-4 (how many leaves perforated by a stake at that point) | | Palms | count of all palms without stems in ne quadrant | | Vines | count of all vines in ne quadrant | | 1VEG 0.5\_3 | yes or no for presence of vegetation from 0.5-3m at canopy point 1 | | 2VEG 0.5\_3 | yes or no for presence of vegetation from 0.5-3m at canopy point 2 | | 3VEG 0.5\_3 | yes or no for presence of vegetation from 0.5-3m at canopy point 3 | | 4VEG 0.5\_3 | yes or no for presence of vegetation from 0.5-3m at canopy point 4 | | 1VEG 3\_10 | yes or no for presence of vegetation from 3-10m at canopy point 1 | | 2VEG 3\_10 | yes or no for presence of vegetation from 3-10m at canopy point 2 | | 3VEG 3\_10 | yes or no for presence of vegetation from 3-10m at canopy point 3 | | 4VEG 3\_10 | yes or no for presence of vegetation from 3-10m at canopy point 4 | | 1VEG 10\_20 | yes or no for presence of vegetation from 10-20m at canopy point 1 | | 2VEG 10\_20 | yes or no for presence of vegetation from 10-20m at canopy point 2 | | 3VEG 10\_20 | yes or no for presence of vegetation from 10-20m at canopy point 3 | | 4VEG 10\_20 | yes or no for presence of vegetation from 10-20m at canopy point 4 | Missing data: na Data was derived from the following sources: * COHN-HAFT, M., A. WHITTAKER, AND P. C. STOUFFER. 1997. A new look at the 'species-poor' central Amazon: The avifauna north of Manaus, Brazil. *In *J. V. Remsen (Ed.). Studies in Neotropical ornithology honoring Ted Parker, Ornithological Monograph No. 48, pp. 205-235. American Ornithologists' Union, Washington. * VAN DER HOEK, Y., G. V. GAONA, AND K. MARTIN. 2017. The diversity, distribution and conservation status of the tree-cavity-nesting birds of the world. Diversity and Distributions 23: 1120-1131. * JOHNSON, E. I., P. C. STOUFFER, AND C. F. VARGAS. 2011. Diversity, biomass, and trophic structure of a central Amazonian rainforest bird community. Revista Brasileira de Ornitologia 19: 1-16.