Genetic variability and telomeres: Insights from a tropical avian hybrid zone
Data files
Jul 15, 2024 version files 73.17 KB
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interplate.repeatability.manacus.telomere.data.csv
9.04 KB
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manacus.telomere.data.031823.csv
8.56 KB
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manacus.telomere.dynamics.031623.csv
2.54 KB
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README.md
5.98 KB
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technical.repeatability.manacus.telomere.data.csv
47.06 KB
Abstract
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.
README: 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).
Scripts used for bioinformatics and processing of genomic data can be found at (https://github.com/kiralong).