Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ...
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of d...
Main Authors: | , , , |
---|---|
Format: | Dataset |
Language: | English |
Published: |
Dryad
2017
|
Subjects: | |
Online Access: | https://dx.doi.org/10.5061/dryad.t8ph5 https://datadryad.org/stash/dataset/doi:10.5061/dryad.t8ph5 |
id |
ftdatacite:10.5061/dryad.t8ph5 |
---|---|
record_format |
openpolar |
spelling |
ftdatacite:10.5061/dryad.t8ph5 2024-06-09T07:44:56+00:00 Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... Attard, Catherine R.M. Beheregaray, Luciano B. Moller, Luciana M. Attard, Catherine R. M. 2017 https://dx.doi.org/10.5061/dryad.t8ph5 https://datadryad.org/stash/dataset/doi:10.5061/dryad.t8ph5 en eng Dryad https://dx.doi.org/10.1111/1755-0998.12739 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 pedigree low coverage relationships Next-generation sequencing Balaenoptera musculus Holocene double-digest restriction-site associated DNA ddRAD Dataset dataset 2017 ftdatacite https://doi.org/10.5061/dryad.t8ph510.1111/1755-0998.12739 2024-05-13T11:05:16Z There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We ... : SNP genotypesGenotype data in COANCESTRY format for 8,294 SNPsCOANCESTRY_input.txtMicrosatellite genotypeGenotype data for one individual at 20 microsatellites. The microsatellite genotypes for the remaining individuals are available in a previous Dryad entry, doi:10.5061/dryad.8m0t6 . The format of the data in the current Dryad entry is the same as the previous entry, except in the current entry there is no sex data column.Microsatellite_genotype.txt ... Dataset Balaenoptera musculus DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
pedigree low coverage relationships Next-generation sequencing Balaenoptera musculus Holocene double-digest restriction-site associated DNA ddRAD |
spellingShingle |
pedigree low coverage relationships Next-generation sequencing Balaenoptera musculus Holocene double-digest restriction-site associated DNA ddRAD Attard, Catherine R.M. Beheregaray, Luciano B. Moller, Luciana M. Attard, Catherine R. M. Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
topic_facet |
pedigree low coverage relationships Next-generation sequencing Balaenoptera musculus Holocene double-digest restriction-site associated DNA ddRAD |
description |
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We ... : SNP genotypesGenotype data in COANCESTRY format for 8,294 SNPsCOANCESTRY_input.txtMicrosatellite genotypeGenotype data for one individual at 20 microsatellites. The microsatellite genotypes for the remaining individuals are available in a previous Dryad entry, doi:10.5061/dryad.8m0t6 . The format of the data in the current Dryad entry is the same as the previous entry, except in the current entry there is no sex data column.Microsatellite_genotype.txt ... |
format |
Dataset |
author |
Attard, Catherine R.M. Beheregaray, Luciano B. Moller, Luciana M. Attard, Catherine R. M. |
author_facet |
Attard, Catherine R.M. Beheregaray, Luciano B. Moller, Luciana M. Attard, Catherine R. M. |
author_sort |
Attard, Catherine R.M. |
title |
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
title_short |
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
title_full |
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
title_fullStr |
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
title_full_unstemmed |
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
title_sort |
data from: genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias ... |
publisher |
Dryad |
publishDate |
2017 |
url |
https://dx.doi.org/10.5061/dryad.t8ph5 https://datadryad.org/stash/dataset/doi:10.5061/dryad.t8ph5 |
genre |
Balaenoptera musculus |
genre_facet |
Balaenoptera musculus |
op_relation |
https://dx.doi.org/10.1111/1755-0998.12739 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.t8ph510.1111/1755-0998.12739 |
_version_ |
1801373829970264064 |