DOI: 10.5061/dryad.wwpzgmsv6
title: Data from: Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores

description: Anthropogenic pressures such as hunting are increasingly driving the
 localized functional extinctions of large- and medium-sized wildlife in
 tropical forests, a phenomenon broadly termed ‘defaunation’. Concurrently
 in these areas, smaller-bodied species benefit from factors such as
 competitive release and increase in numbers. This transformation of the
 wildlife community can impact species interactions and ecosystem services
 such as seed dispersal and seed-mediated geneflow with far reaching
 consequences. Evidence for negative genetic effects following defaunation
 is well-documented in large-seeded plants that require large frugivores
 for long distance seed dispersal. However, how defaunation affects plants
 with small or medium-small seeds (&lt; 1.5cm), which tend to be
 consumed and dispersed by frugivorous mutualists of a range of body-sizes
 and responses to anthropogenic threats, is not well understood. To better
 understand defaunation’s impacts on tropical plant communities, we
 investigated spatial and genetic patterns in a hyperabundant
 medium-to-small-seeded palm, Euterpe precatoria in three sites with
 different defaunation levels. Results indicate that defaunation is
 associated with higher fine-scale spatial genetic structure among
 seedlings and increased spatial clustering within seedling cohorts and
 between seedlings and conspecific adults, as well as a reduction in
 nearest-neighbor distances between seedlings and conspecific adults. There
 were no clear effects on inbreeding or genetic diversity. However, we
 caution these trends may indicate that defaunation reduces seed dispersal
 services for species previously presumed to be robust to deleterious
 effects of losing large frugivores by virtue of having smaller seeds and
 broad suites of dispersal agents, and negative downstream effects on
 genetic diversity could occur.
description: # Data from: Defaunation increases clustering and fine-scale spatial
 genetic structure in a small-seeded palm despite remaining small-bodied
 frugivores
 [https://doi.org/10.5061/dryad.wwpzgmsv6](https://doi.org/10.5061/dryad.wwpzgmsv6) These data are used in Lamperty et al 2024, Molecular Ecology, entitled "Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores". This study investigated the effects of defaunation and reductions in local frugivore abundances on seed-dispersal services and seed-mediated gene flow for a relatively small-seeded palm species, Euterpe precatoria. In 3 different sites in Madre de Dios, Peru (located in the western Amazon Basin) that varied in exposure to hunting, we mapped the location of all seedling (&lt; 1 m tall) and adult ( &gt; 10cm diameter at breast height) E. precatoria within long-term 4-ha forest study plots. For each E. precatoria found, we recorded their height and took fresh tissue samples from each individual. From each plot, DNA was extracted from a random subset of ~125 seedlings and all adults for subsequent genetic analysis. Mapping was accomplished via establishing an 'origin' at the SW corner for each 4-ha plot, which corresponds to X, Y point 0, 0. Mapping was accomplished by dividing the 4-ha plots into smaller 5m x 5m grids that were thoroughly searched. The locations of E. precatoria were recorded relative to the SW origin corner (0,0) and given X and Y coordinates corresponding to the distances, in meters, each individual was to the East (X) and North (Y) of the 0,0 origin. We used microsatellite markers to genotype individuals, and individual allele data are included in the dataset. We subsequently checked marker quality (Hardy-Weinberg Equilibrium, Linkage Disequilibrium, Null Alleles) to judge which may be problematic markers that should be excluded from genetic analyses. The 3 sites are and their defaunation levels were: 1\. Reserva Amazonica ('RA' in the dataset); highly defaunated. 2\. Los Amigos ('LA' in the dataset); intermediately defaunated/recovering. 3\. Tambopata Research Center ('TRC' in the dataset); faunally-intact and highly protected from hunting. **Description of the data and file structure** The data is available in a single spreadsheet with 5 tabs. Tab 1: the height data, in meters, of each seedling and the corresponding site (SITE) and individual ID (ID). Each E. precatoria in each site has a unique ID. Tab 2: the genotype data and the location data for the individuals that were genotyped. X and Y correspond to the distance to the East and North, respectively, in meters, each individual was from the SW corner of the plot (which corresponds to 0, 0). These data were used to compute pairwise distances between individuals. Again, the stage (STAGE) and individual ID (ID) for each site (SITE) are given. Then, the alleles are given for each marker for each individual. Repeated numbers in two columns adjacent columns with the same marker name (e.g., Ep05) are homozygotes, and different numbers are heterozygotes. Cells populated with 'NULL' are instances where amplification likely failed and a given allele could not be identified with certainty. Stage (STAGE) is also given (seedling or adult). Tabs 3-5: these tabs include the spatial data (in the same X, Y format as described above) for all seedlings and adults in each of the 3 plots, rather than just the random 125 subset + adults that were genotyped. **Sharing/Access information** This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any. Links to other publicly accessible locations of the data: \- Access this dataset and code on GitHub: [https://github.com/Jlamperty/Defaunation-SeedDisp-MEC](https://github.com/Jlamperty/Defaunation-SeedDisp-MEC) Preprint link: \- [https://doi.org/10.22541/au.171610931.12239533/v1](https://doi.org/10.22541/au.171610931.12239533/v1)