Niche and neutral-based processes differ in importance for common and rare species in a metacommunity of anurans in subtropical grasslands
Data files
Mar 06, 2024 version files 36.18 KB
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Data_and_script_for_common_and_rare_species.rar
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README.md
Abstract
Most species-rich communities consist of a limited number of common species and many rare species. This widespread ecological pattern can arise due to the predominance of either niche-based or neutral-based processes in community structuring. We tested two hypotheses related to this pattern for an anuran metacommunity composed of 35 species distributed in 187 ponds in the South Brazilian grasslands: (1) for common species, niche processes should prevail over neutral ones because common species evolved under a wider range of ecological filters than rare species; (2) for rare species, neutral processes should prevail because rare species are more prone to ecological drift and dispersion limitation. We found that the densities of both common (i.e., the 25% higher density ones) and rare (i.e., the 75% lower density ones) species depended mostly on pond structure and land use, indicating a similar response to niche-based processes in both groups of species. The importance of pond descriptors and type of land use, however, differed between the two groups, confirming that common and rare species represent ecologically distinct groups within the metacommunity. In addition, neutral processes—related to dispersion limitation or not—influenced both species groups, but the spatial filters selected explained a smaller portion of the variation in species densities compared to environmental descriptors. Our findings showcase the prevalence of niche processes in structuring communities of common and rare species of anurans in subtropical grasslands and indicate the variables of pond structure and land use that are relevant to guide conservation practices for the metacommunity of anurans in the South Brazilian grasslands.
README
The zip file contains five groups of txt files containing all the data and scripts used in the analyses of the manuscript. Analyses were conducted for both common and rare species. The five groups of files are:
Group 1: contains data on the geographic coordinates of each pond used. Latitude and longitude are in the columns, and the ponds are in the rows. File names:
coord.common
coord.rare
Group 2: contains species density data for each pond used. The species are in the columns, and the ponds are in the rows. File names:
dens.common
dens.rare
The abbreviation of species names is given below:
Dmin Dendropsophus minutus
Dnan Dendropsophus nanus
Dsan Dendropsophus sanborni
Ebic Elachistocleis bicolor
Hlep Boana leptolineata
Hpul Boana pulchella
Lcha Leptodactylus macrosternum
Lfus Leptodactylus fuscus
Lgra Leptodactylus gracilis
Llati Leptodactylus latinasus
Llatr Leptodactylus luctator
Lmys Lepdodactylus mystacinus
Lpla Leptodactylus plaumanni
Matr Melanophryniscus atroluteus
Oame Odontophynus asper
Pbil Physalaemus biligonigerus
Pcar Pseudis cardosoi
Pcfg Physalaemus carrizorum
Pcuv Physalaemus cuvieri
Pfal Pseudopaludicola falcipes
Pgra Physalaemus gracilis
Pihe Phyllomedusa iheringii
Plis Physalaemus lisei
Pmin Pseudis minuta
Prio Physalaemus riograndensis
Rfer Rhinella dorbignyi
Rict Rhinella icterica
Rsch Rhinella diptycha
Sfus scinax fuscovarius
Sgra Scinax granulatus
Snas Scinax nasicus
Sper Scinax perereca
Spin Scinax pinima
Ssqu Scinax squalirostris
Suru Scinax uruguayus
Group 3: contains data on landscape variables for each pond used. The landscape descriptors are in the columns and the ponds in the lines. File names:
landscape.common
landscape.rare
Below we present the specifications of each landscape variable evaluated for each buffer zone 1, 3, and 5 Km, i.e., we measured each of the landscape descriptors for the three buffer zones of 1, 3, and 5 km (for more detail, see Supplementary Material 2):
Agriculture (1, 3, 5 km): total area of annual crop
Forest (1, 3, 5 km): total area of native forest
Grassland (1, 3, 5 km): total area recognizable as a native grassland
Rock outcrop (1, 3, 5 km): total area of rocks
Silviculture (1, 3, 5 km): total area of pine, eucalyptus, or acacia plantation
Sandy (1, 3, 5 km): total area of beaches, and or sandy soil
Urban (1, 3, 5 km): total urban area
Water (1, 3, 5 km): total area of water surface free of emergent vegetation
Wetland (1, 3, 5 km): freshwater marshes with typical presence of aquatic vegetation
Group 4: contains data on local variables for each pond used. The local descriptors are in the columns, and the ponds are in the rows. File names:
local.common
local.rare
Below we present the specifications of each local variable evaluated (for more detail, see Supplementary Material 1):
Depth: Mean water depth
Temperature: Air temperature
Humidity: Air relative humidity
pH: Water pH
Conductivity: Water conductivity
Dissolved oxygen: Water dissolved oxygen
Water turbidity: Water turbidity
Forest: Forest considering a buffer zone of 50 m around the pond
Grassland: Grassland in a buffer zone of 50 m around the pond
Agriculture: Agriculture in a buffer zone of 50 m around the pond
Pasture: Planted pasture in a buffer zone of 50 m around the pond
Edge 1: Number of edge types
Edge 2: Edge without vegetation and dry soil
Edge 3: Edge with vegetation and dry soil
Edge 4: Edge without vegetation and humid soil
Edge 5: Edge with vegetation and humid soil
Edge 6: Edge without vegetated and flooded soil
Edge 7: Edge with vegetated and flooded soil
Edge 8: Flat edge (180°)
Edge 9: Sloping edge (45°)
Edge 10: Steep edge (90°)
Edge vegetation 1: Number of vegetation strata on the edge
Edge vegetation 2: Creeping-herbaceous vegetation (up to 30 cm) on edge
Edge vegetation 3: Creeping-herbaceous (up to 30 cm) on edge
Edge vegetation 4: Herbaceous-shrub (31 to 70 cm) on edge
Edge vegetation 5: Shrub (71 to 99 cm) on edge
Shadow: Shadow in the water surface
Emergent plant: Emerging hydrophytes
Aquatic vegetation 1: Number of vertical vegetation strata on the water surface
Aquatic vegetation 2: Vegetation up to 30 cm
Aquatic vegetation 3: Vegetation from 31 cm to 60 cm
Aquatic vegetation 4: Vegetation greater than 1 m
Invertebrates: Presence of predatory invertebrates
Fish: Presence of predatory fish
Photoperiod: Length of day
Moon: Lunar disk percentage
5) We present the R script for analysis. Below is a description of each file:
script common x rare - here, we present all the steps for RDA analysis.
script Graphics - here, we present all the steps for build Graphics.
script MEM - here, we present all the steps for build MEM.
Methods
The study was conducted in the South Brazilian grasslands located in the state of Rio Grande do Sul, Brazil. Data were collected from 187 ponds using the 'survey at breeding sites' method.
For each pond, 36 environmental descriptors were measured. To accomplish this, we visually measured each of the 34 pond descriptors (e.g., type of pond edge, depth, area, type of vegetation, pH, turbidity) following the methodology outlined by Iop et al. (2020). Additionally, we recorded two variables related to the sampling date that could potentially impact the number of records: the length of the photoperiod and the percentage of lunar disk (moon phase).
Landscape descriptors were determined through digital land use and land cover (LULC) mapping for the Landscape Sampling Units (LSUs), considering the base years of 2002. The scale was based on two false-color compositions. These landscape descriptors correspond to the area of each LULC class around each LSU. We employed three buffer zones (1 km, 3 km, and 5 km) to calculate these descriptors, taking into account the reported anuran dispersion range in the literature, which varies between 400 m and 10 km. In total, nine landscape descriptors (Agriculture, Forest, Pasture, Rocky Outcrop, Sandy, Forestry, Urban, Water, and Wetland) were measured within the buffers generated by the three rays.
To assess whether geographic space influences the distribution of common and rare species in the metacommunity, we generated Moran’s eigenvector maps (MEM) using the geographic coordinates of each pond as a proxy for spatial patterns related to dispersion and ecological drift.
Redundancy analysis (RDA) was employed to evaluate the role of environmental characteristics (local and landscape descriptors) and spatial patterns in the organization of the common and rare anuran community. RDA combines multiple regression with principal component analysis to identify a series of linear combinations of explanatory variables (i.e., local environmental descriptors, landscape descriptors, and spatial filters) that best explain the variation in the response matrix (i.e., density of species in each survey site).