Dataset DOI: 10.5061/dryad.47d7wm3wm

Description of the data and file structure

Microsatellite genotype data for the Turquoise-fronted Amazon (Amazona aestiva)

Dataset description

This dataset contains microsatellite genotype data generated and analyzed in the study of reproductive strategies and breeding-site fidelity in the socially monogamous Turquoise-fronted Amazon (Amazona aestiva).

Samples were obtained from wild A. aestiva associated with nesting cavities monitored in the Federal District, Brazil, and Chaco Province, Argentina.

The dataset contains multilocus genotypes at six microsatellite loci and associated information on manuscript cavity identification, original field cavity identification, sample identification, and sampling year.

The microsatellite data were used to investigate genetic relatedness and parentage within broods and to evaluate reproductive patterns, including extra-pair paternity.

File included

JFO-2026-804_dryad_data.csv

This is the primary data file containing the microsatellite genotype matrix and associated sampling information.

• File format: CSV
• Field delimiter: semicolon (;)
• Number of columns: 16
• Number of individual samples: 87
• Number of physical rows in the CSV file: 116
• Sampling locations: Federal District, Brazil, and Chaco Province, Argentina
• Microsatellite loci: 6
• Genotype columns: 12 (two allele columns per locus)

The 116 physical rows include blank separator rows and geographic section labels used to organize the original dataset. These rows do not represent individual samples. Individual records are identified by a non-empty value in the Sample ID column.

For analysis, users should retain only rows containing a Sample ID.

Geographic organization of the dataset:

The CSV is organized into two geographic sections:

1. Distrito Federal/Brazil
2. Província del Chaco/Argentina

The geographic section labels are included as organizational rows in the CSV and do not represent samples.

There are 47 individual samples from the Federal District, Brazil, and 40 individual samples from Chaco Province, Argentina.

Important note about cavity identifiers:

Cavity identifiers such as N01, N02, etc. are not globally unique across the entire dataset because similar numbering was used in the two geographic regions.

Therefore, the geographic section should be considered when interpreting Cavity ID Manuscript.

For example, an N01 cavity in Brazil, if present, should not automatically be considered the same nesting cavity as an N01 cavity in Argentina.

Variables and column descriptions

The CSV contains the following 16 columns.

Genotype coding

Each individual is diploid, and the two alleles observed at each microsatellite locus are provided in separate columns.

Alleles are reported as allele-size values according to the microsatellite genotyping procedure used in the study.

Missing or unavailable genotypes are represented as 0, where applicable.

Sampling information

The dataset includes samples associated with monitored nesting cavities. Cavity identifiers are provided both as the manuscript cavity identification and, where applicable, the original field cavity identification.

Sampling years represented in the dataset are 2004–2008.

The dataset contains records associated with 18 nesting cavities and 87 unique sample identifiers. The number of records reflects the sampling structure and repeated information associated with the study design.

Microsatellite loci

Six microsatellite loci were used:

• AgGT 07
• AgGT 12
• AgGT 21
• AgGT 29
• AgGT72
• AgGT83

Microsatellite genotype coding

The genotype values are reported as allele-size values generated during microsatellite genotyping.

For each locus:

• the _1 column represents one allele;
• the _2 column represents the second allele;
• identical values in the two allele columns indicate a homozygous genotype;
• different values indicate a heterozygous genotype.

For example, an individual with:

AgGT 07_1 = 262

and

AgGT 07_2 = 272

has a heterozygous genotype with allele sizes 262 and 272 at AgGT 07.

Allele-size values are microsatellite allele states and should not be interpreted as continuous quantitative measurements.

Missing and unavailable data

Empty cells occur in the dataset and should be treated as missing information unless otherwise specified by the associated sampling structure.

The dataset also contains the numeric value 0 in some microsatellite genotype fields, particularly at AgGT 12, AgGT 21, and AgGT83.

Users should consult the associated publication and genotyping records before interpreting 0 as a biological allele, missing genotype, or other coding category.

The value 0 should therefore not automatically be converted to NA without confirming its intended meaning in the original genotyping dataset.

Rows without a Sample ID are organizational rows and should not be interpreted as missing individual samples.

Data structure

The dataset is organized at the individual-sample level.

Each individual sample is represented by one row containing:

1. cavity information;
2. sample identification;
3. genotypes at six microsatellite loci;
4. sampling year when available.

Thus, the 87 individual records provide up to 12 allele observations per individual, corresponding to two alleles at each of the six loci.

Genetic analyses

The microsatellite genotype data were used for analyses of genetic relatedness and parentage. The study employed:

• COLONY 2.0 for sibship and parentage inference;
• ML-Relate for genetic relatedness analyses;
• Genepop for population genetic analyses;
• Micro-Checker for assessment of potential genotyping errors and null alleles;
• Cervus for allele-frequency and parentage-related analyses.

Detailed laboratory procedures, genotyping methods, analytical parameters, and statistical procedures are provided in the associated publication.

Software required for data reuse

The primary data file is a plain-text, semicolon-delimited CSV file and does not require specialized software to open.

The dataset can be imported into:

• Microsoft Excel;
• LibreOffice Calc;
• R;
• Python; or
• other software capable of reading delimited text files.

The original genetic analyses were conducted using the software listed above. Researchers attempting to reproduce the original analyses should consult the associated publication for analytical parameters and software settings.

Data quality and considerations for reuse

The dataset contains 87 individual sample records and six microsatellite loci.

Users reanalyzing these data should consider:

• missing genotype information;
• the presence of numeric 0 values in some genotype fields;
• the distinction between Brazilian and Argentine sampling locations;
• the fact that cavity identifiers may be reused between geographic regions;
• the difference between Cavity ID Manuscript and Field cavity; and
• the sampling years available for each geographic region.

The microsatellite allele values represent allele-size states generated through the genotyping procedure and should be treated as categorical allele states in downstream genetic analyses.

Researchers conducting independent analyses should evaluate genotype completeness, potential genotyping errors, allele frequencies, and the suitability of the six loci for their specific analytical objectives.

Associated publication

The dataset is associated with:

Genetic evaluation of reproductive strategies and breeding-site fidelity in the socially monogamous Turquoise-fronted Amazon (Amazona aestiva, Psittaciformes: Aves).

Journal of Field Ornithology.

The final bibliographic information and article DOI should be added once the article has been formally published.

Recommended citation

Users should cite both the Dryad dataset and the associated publication when using these data

Data reuse

These data may be reused for research involving microsatellite-based genetic analyses, genetic relatedness, parentage, mating systems, reproductive strategies, and population genetics of Amazona aestiva.

Contact

For questions regarding the dataset, please contact the corresponding author of the associated publication.

Access information

The data in this submission were generated specifically for this study and were not derived from previously published or publicly available datasets. No external data sources were used.