Data from: Unraveling the genetic parameters, social relationships and conservation aspects of a group of Touit melanonotus ( Brown-backed Parrotlet)
Data files
Jun 23, 2025 version files 30.05 MB
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2touit_snps_total.vcf
11.81 MB
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HeFiltered_NotFiltered.csv
4.50 KB
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kinship.csv
16.25 KB
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pop_info_touit_out.csv
898 B
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pop_info_touit.csv
1.01 KB
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README.md
5.32 KB
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sambar_Touit.R
2.79 KB
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snpfiltr_touit.R
3.12 KB
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stairway_sambar_touit.R
3.80 KB
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touit_filt2_95_out.vcf
1.04 MB
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Touit_mel.blueprint
1.57 KB
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touit_qual_filt2_75.vcf
1.28 MB
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touit_snps_total_out.vcf
15.89 MB
Abstract
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.
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
Steps
- Filter VCF files using
snpfiltr_touit.R. - Run kinship and diversity analyses with
sambar_Touit.R. - Perform demographic inference using
stairway_sambar_touit.Rwith the filtered data andTouit_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