DOI: 10.5061/dryad.n02v6wx6g
title: Recovery of lizard assemblages ten years after reduced-impact logging in central-eastern Amazonia

description: Understanding changes in species composition due to human-induced habitat
 modification and environmental filtering is essential for formulating
 effective conservation strategies. Species turnover resulting from
 reduced-impact logging (RIL) is expected in the short term, generally with
 species adapted to open areas replacing those dependent on old-growth
 forest. However, little is known about how RIL activities influence
 assemblages after the perturbation ceased. We sampled lizards across an
 edaphic and vegetation-structure gradient in 64 plots in the Brazilian
 Amazon to test the hypothesis that changes in assemblage composition and
 proportion of heliothermic species are due to canopy openness resulting
 from ceased RIL activities and individual tree falls, or to other
 environmental gradients. Contrary to expectations, canopy openness did not
 significantly affect the overall composition of lizard assemblages, but
 nearby unforested areas influenced assemblage composition, resulting in a
 higher proportion of heliothermic species. The composition of lizard
 assemblages was also significantly influenced by the distance to the
 nearest water body, vegetation height, and soil sand content. However,
 leaf-litter height did not have a detectable impact on the composition of
 lizard assemblages. We conclude that short-term changes in species
 composition due to habitat modification by RIL do not persist in the long
 term after the perturbation ceases, and the assemblages may recover as
 vegetation regenerates. Although lizard species respond to spatial and
 temporal variation in environmental characteristics, we found evidence
 that lizard assemblages recover as reduced-impact logging (RIL) activities
 cease and vegetation regenerates.
description: We sampled lizards across an edaphic and vegetation-structure
 gradient in 64 plots. In the southern portion of the study region, inside
 the Tapajós National Forest (TNF), we sampled 40 plots distributed across
 four research modules established as part of the Brazilian Program for
 Biodiversity Research (PPBio) for biodiversity monitoring. These modules
 follow the Rapid Assessment and Long-term Ecological Research (RAPELD)
 system (Magnusson et al., 2013). Each module is 1 km in width and 5 km in
 length. Within each module, there are 10 evenly spaced 250-m-long plots
 that follow terrain contours (Magnusson et al., 2013). The minimum
 distance between plots in the same module is 1 km. In the north of the
 study area, inside the Alter do Chão APA, we also surveyed 24 plots, 19
 located in forest fragments surrounded by a savanna matrix and five in
 continuous forest (Figure 1). Although these plots were 250 meters long,
 they did not follow the terrain contour. However, since the area was
 relatively flat, this deviation resulted in minimal differences in
 variability within each plot. We used data collected by
 a portable Light Detection and Ranging (LIDAR) device (Model
 LD90-3100VHS-FLP, Riegl, Horn, Austria), which employs laser scanning to
 measure variables that quantify canopy openness (our local-clearing index)
 and average vegetation height in the plots (see Torralvo et al., 2020;
 Torralvo et al., 2021). We estimated canopy openness by calculating the
 percentage of sky shots, which represents the number of emitted pulses
 that do not return to the apparatus. Measures of
 unforested areas, the proportion of open areas in the landscape, were
 obtained in a previous study (Torralvo et al., 2020; Torralvo et al.,
 2021) by using a satellite-based layer with 30 m x 30 m pixels made
 available through the MapBiomas project (Souza et al., 2020, see full
 description in http://mapbiomas.org), which summarized the data on area
 without forest until 2019. Using the raster R-package (Hijmans, 2020), we
 extracted the proportions of areas without forest within 500-meter buffers
 around each plot. In our study region, unforested areas are predominantly
 found in the northern part. Soil collection and
 analyses were carried out following the PPBio protocol (available at
 https://ppbio.inpa.gov.br/manuais). We used data on the quantity (g/kg) of
 clay and sand (sum of fine and coarse sand) to 5 cm from the surface.
 Leaf-litter height was measured with a ruler at six points separated by
 50-meter intervals in each plot and the mean values per plot were used in
 the analyses. We measured the distances from each plot to the nearest
 water body using the Euclidean distance matrix tools of QGIS 3.16.2
 software (QGIS Development Team, 2020), applied to combined hydrographic
 shapefiles from public repositories (IBGE, 2021)
description: # Recovery of lizard assemblages ten years after reduced-impact logging in
 central-eastern Amazonia
 [https://doi.org/10.5061/dryad.n02v6wx6g](https://doi.org/10.5061/dryad.n02v6wx6g) ## Description of the data and file structure These data were collected in 64 plots organized into 40 plots across four modules (with 10 plots in each module) from Tapajós National Forest and 24 plots in Alter do Chão Village, Pará state, Brazil. The file refers to data on the abundance of lizard species found at the sites and metrics of environmental variables.   **File - Ganança_et_al_data_I** | **Columns ID** | **Description** | | :--------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Site | Identification or name of each sampling area. | | Plot | Identification or name of each sampled plot. The naming code reflects the module identification followed by the module line identification and sampled plot. | | Lat | Latitude of the geographical coordinate collected for each sampled plot in decimal degrees. | | Long | Longitude of the geographical coordinate collected for each sampled plot in decimal degrees. | | Unforested | Unforested areas proportion data obtained for each sampled plot (see methods). | | Litter | Litter depth data (in cm) obtained for each sampled plot (see methods). | | log\_Dist\_water | Log Distance to water bodies data (in m) obtained each sampled plot (see methods). | | Sand | Sand soil content data (in g-kg) obtained for each sampled plot (see methods). | | Silt | Silt soil content data (in g-kg) obtained for each sampled plot (see methods). | | H.MEAN.Loess | average vegetation height (m) in the plots (see methods). | | P.P.skyshots | Percentage of sky shots (%), which represents the number of emitted pulses that do not return to the apparatus (see methods). | | Gonatodes\_humeralis through Arthrosaura\_reticulata | Name of each species sampled. The naming found in the colums reflects the taxonomic identification at the species level with the abundance (total number of records) in the lines, for each sampled plot (see methods). |