DOI: 10.5061/dryad.ht76hdrts
title: Data from: Unraveling the genetic parameters, social relationships and conservation aspects of a group of Touit melanonotus ( Brown-backed Parrotlet)

description: The genetic parameters underlying the biological and behavioral traits of
 most Neotropical parrots are poorly understood due to limited sampling.
 Touit melanonotus is a globally Near Threatened, rare, unobtrusive, and
 small-bodied parrotlet endemic to the Atlantic Forest of Brazil. In 2020,
 a flock of T. melanonotus collided with a window at São Paulo
 International Airport in Guarulhos, São Paulo State, Brazil, resulting in
 the death of 29 individuals. We aimed to assess the genetic diversity of
 this flock, estimate the effective population size, and conduct a pairwise
 kinship analysis to explore flock formation, behavior, and the familial
 structure of this species. To that end, we used single-nucleotide
 polymorphisms (SNPs) derived from genome-wide ultraconserved elements
 (UCEs) of the flock. We observed a higher than expected genetic diversity
 (t = 7.243, p~0) and no evidence of inbreeding depression, with F ranging
 from -0.406 to -0.110 (χ2 = 37.687, p = 0; χ2 = 4.217, p = 0.040,
 respectively). We identified evidence of a historical decline in the
 effective population size of wild individuals, and kinship analysis
 indicated the presence of different familial nuclei, with multiple
 individuals pairing with more than one partner in the sampled group, which
 is strong evidence for extra-pair copulation that may help maintain
 heterozygosity levels in this declining population. Based on our genetic
 parameters, we found no immediate or urgent need for genetic management as
 a conservation action. We recommend that conservation efforts focus on
 habitat maintenance and the restoration of the Atlantic Forest, a highly
 degraded and fragmented biome.
description: # Unraveling the genetic parameters, social relationships and conservation
 aspects of a group of Touit melanonotus ( Brown-backed Parrotlet)
 Published in *Ornithological Applications*, 2025 #### Repository Contents
 This repository contains the input files, scripts, and result summaries
 used in the analyses described in the manuscript. **Files Included** |
 File | Description | | ---------------------------- |
 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `2touit_snps_total.vcf` | Raw SNP matrix (VCF format) before any filtering. | | `touit_qual_filt2_75.vcf` | Filtered SNP matrix (75% completeness), used for diversity and kinship analyses. | | `touit_filt2_95_out.vcf` | Filtered SNP matrix (95% completeness), used for Stairway Plot demographic inference. | | `touit_snps_total_out.vcf` | Raw SNP matrix including outgroup samples, before filtering. | | `snpfiltr_touit.R` | R script for SNP filtering using the SNPfiltR package. | | `sambar_Touit.R` | R script for diversity and kinship analyses using SambaR. | | `stairway_sambar_touit.R` | R script for demographic inference with Stairway Plot and SambaR. | | `Touit_mel.blueprint` | Input blueprint file for Stairway Plot. | | `HeFiltered_NotFiltered.csv` | Summary statistics of genetic diversity for *Touit melanonotus* individuals, comparing the dataset filtered for heterozygosity and the non-filtered dataset. See details below. | | `kinship.csv` | Raw pairwise kinship analysis results for the filtered *T. melanonotus* dataset. See details below. | | `pop_info_touit.csv` | Population table used in `sambar_Touit.R`. | | `pop_info_touit_out.csv` | Population table used in `stairway_sambar_touit.R`. | #### **File Details** #### `HeFiltered_NotFiltered.csv` Summary statistics of genetic diversity for *Touit melanonotus* individuals, comparing the dataset filtered for heterozygosity and the non-filtered dataset. * **name** – Sample name. * **hetero** – Observed heterozygosity (*He*), representing the proportion of heterozygous loci in each individual. * **expHe** – Expected heterozygosity under Hardy-Weinberg equilibrium. * **F** – Inbreeding coefficient (*F*), measuring deviation from Hardy-Weinberg equilibrium; negative values indicate excess heterozygosity. * **F_pvalue** – p-value associated with the inbreeding coefficient (*F*), indicating its statistical significance. The left side of the table corresponds to the dataset **filtered for heterozygosity**, while the right side corresponds to the **non-filtered dataset**. #### `kinship.csv` Raw pairwise kinship analysis results for the filtered *T. melanonotus* dataset. * **Ind1** and **Ind2** – Sample IDs for pairwise comparisons; sample assignments match those in `pop_info_touit.csv`. * **r0**, **r1**, **kingrobust**, **k0** – Kinship statistics derived from the KING-robust method. * For details on the KING-robust algorithm, see Manichaikul et al. (2010) (reference below). How to Run the Analyses #### Requirements * R ≥ 4.x * R packages: `SNPfiltR`, `SambaR`, `vcfR`, `tidyverse` * [Stairway Plot v2](https://github.com/xiaoming-liu/stairway-plot-v2) ### Steps 1. Filter VCF files using `snpfiltr_touit.R`. 2. Run kinship and diversity analyses with `sambar_Touit.R`. 3. Perform demographic inference using `stairway_sambar_touit.R` with the filtered data and `Touit_mel.blueprint`. #### **Reference** Manichaikul, A., Mychaleckyj, J. C., Rich, S. S., Daly, K., Sale, M., & Chen, W. M. (2010). Robust relationship inference in genome-wide association studies. *Bioinformatics*, 26(22), 2867–2873. [https://doi.org/10.1093/bioinformatics/btq559](https://doi.org/10.1093/bioinformatics/btq559)