DOI: 10.5061/dryad.qnk98sfnh
title: Genetic variability and telomeres: Insights from a tropical avian hybrid zone

description: Telomere lengths and telomere dynamics can correlate with lifespan,
 behavior, and individual quality. Such relationships have spurred interest
 in understanding variation in telomere lengths and their dynamics within
 and between populations. Many studies have identified how environmental
 processes can influence telomere dynamics, but the role of genetic
 variation is much less well characterized. To provide a novel perspective
 on how telomeric variation relates to genetic variability, we
 longitudinally sampled individuals across a narrow hybrid zone (n = 127
 samples), wherein two Manacus species characterized by contrasting
 genome-wide heterozygosity interbreed. We measured individual (n = 66) and
 population (n = 3) differences in genome-wide heterozygosity and, among
 hybrids, amount of genetic admixture using RADseq-generated SNPs. We
 tested for population differences in telomere lengths and telomere
 dynamics. We then examined how telomere lengths and telomere dynamics
 covaried with genome-wide heterozygosity within populations. Hybrid
 individuals exhibited longer telomeres, on average, than individuals
 sampled in the adjacent parental populations. No population differences in
 telomere dynamics were observed. Within the parental population
 characterized by relatively low heterozygosity, higher genome-wide
 heterozygosity was associated with shorter telomeres and higher rates of
 telomere shortening – a pattern that was less apparent in the other
 populations. All of these relationships were independent of sex, despite
 the contrasting life histories of male and female manakins.  Our
 study highlights how population comparisons can reveal interrelationships
 between genetic variation and telomeres, and how naturally occurring
 hybridization and genome-wide heterozygosity can relate to telomere
 lengths and telomere dynamics.
description: # Genetic variability and telomeres: Insights from a tropical avian hybrid
 zone This data contains telomere length measurements from Manacus
 vitelinus, candei, and their hybrids. Also included are the sex of the
 individuals, their age, and location of their capture. For a subset of the
 individuals, genomic data was used to quantify a genome-wide
 heterozygosity estimate and, for hybrids, a hybrid index. Some data files
 are also used to assess the precision of the telomere assay. See script
 and ReadMe.txt file for more information. ## **Description of Software
 Files** **File name:** "manacus.telomere.analysis.R"
 **Description:** R script containing code used to recreate results in
 combination with the following data files.  ## Description of the Data and
 file structure Read me for data files associated with “Genetic Variability
 and Telomeres: Insights from a Tropical Avian Hybrid Zone.” **File name:**
 “Session_info.docx” **Description:** This file includes all the
 information related to the version of R and the packages used to generate
 our results. This can be used to increase the reproducibility of our
 results using the supplied code. **File name:**
 “interplate.repeatability.manacus.telomere.data.csv” **Description:** This
 csv file contains data to estimate the inter-plate repeatability of
 GAPDH/Telomere Cq values and relative telomere length measurements
 **Columns:** plate: ID for qPCR plate well: Position on qPCR ID:
 individual identifier code contents: individual identifier and the year
 the sample was collected, separated by a “.” year: year sample was
 collected dup: denotes if a row is a duplicate of another for samples run
 in duplicate GAPDH.Cq: Cq value for the GAPDH primers GAPDH.Eff:
 well-specific efficiencies for the GAPDH primers gapdh.control:
 plate-specific Cq value for the GAPDH inter-plate control dgapdh:
 difference between inter-plate control and well GAPDH Cq value egapdh:
 well-specific efficiency raised to the power of dgapdh Telo.Cq: Cq value
 for the Telomere primers Telo.Eff: well-specific efficiencies for the
 telomere primers telo.control: plate-specific Cq value for the telomere
 inter-plate control dtelo: difference between inter-plate control and well
 Telomere Cq value etelo: well-specific efficiency raised to the power of
 dtelo rtl: relative telomere length value, calculated by dividing etelo by
 egapdh plate.well: combination of plate and well location population:
 denotes which population the sample belonged to plate.control: denotes if
 the well is a sample run on every plate **File name:**
 “manacus.telomere.data.031823.csv” \**Description: **This file containing
 telomere measurement values and the associated predictor variables.
 **Columns:** group: denotes which of the three populations the row
 corresponds to plate: denotes which plate the sample was measured on ID:
 individual identifier year: year sample was collected rTL: relative
 telomere length age: categorial age of bird when sample collection
 occurred. Can be either definitive, juvenile, or unknown age. sex: sex of
 individual date: date of sample collection hi: hybrid index value htzg_in:
 genome-wide heterozygosity values calculated using all sites, including
 invariant sites. Empty cells are those samples which were not sequenced
 and therefore do not heterozygosity data. htzg_var: genome-wide
 heterozygosity values calculated after excluding invariant sites. Empty
 cells are those samples which were not sequenced and therefore do not
 heterozygosity data. **File name:** “manacus.telomere.dynamics.031623.csv”
 **Description:** This file contains data used to examine telomere dynamics
 **Columns:** plate: qPCR plate used to quantify telomere lengths ID:
 individual identifier group: denotes which of the three populations the
 row corresponds to sex: denotes if the individual is ZZ (male) or ZW
 (female) Time1: telomere measurement at time 1 Time2: telomere measurement
 at time 2 D: annual change in telomere length after correcting for the
 regression to the mean **File name:**
 “technical.repeatability.manacus.telomere.data.csv” **Description:** This
 csv file contains data to estimate the technical repeatability of
 GAPDH/Telomere Cq values and relative telomere length measurements
 **Columns:** plate: ID for qPCR plate well: Position on qPCR ID:
 individual identifier code contents: individual identifier and the year
 the sample was collected, separated by a “.” year: year sample was
 collected dup: denotes if a row is a duplicate of another for samples run
 in duplicate GAPDH.Cq: Cq value for the GAPDH primers GAPDH.Eff:
 well-specific efficiencies for the GAPDH primers gapdh.control:
 plate-specific Cq value for the GAPDH inter-plate control dgapdh:
 difference between inter-plate control and well GAPDH Cq value egapdh:
 well-specific efficiency raised to the power of dgapdh Telo.Cq: Cq value
 for the Telomere primers Telo.Eff: well-specific efficiencies for the
 telomere primers telo.control: plate-specific Cq value for the telomere
 inter-plate control dtelo: difference between inter-plate control and well
 Telomere Cq value etelo: well-specific efficiency raised to the power of
 dtelo rtl: relative telomere length value, calculated by dividing etelo by
 egapdh plate.well: combination of plate and well location population:
 denotes which population the sample belonged to ## Sharing/access
 Information These data are not publicly available in any other location.
 Was data derived from another source? If yes, list source(s): Genomic data
 used to generate heterozygosity estimates and the hybrid index can be
 found on NCBI at,
 ([https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893627?report=overview](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893627?report=overview)). Scripts used for bioinformatics and processing of genomic data can be found at ([https://github.com/kiralong](https://github.com/kiralong)).