Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Abstract Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylo...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Philipp Kirschner, Wolfgang Arthofer, Stefanie Pfeifenberger, Eliška Záveská, Peter Schönswetter, The STEPPE Consortium, Florian M. Steiner, Birgit C. Schlick-Steiner
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6668b00ffc3645e09f78470e07144059
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:6668b00ffc3645e09f78470e07144059
record_format	dspace
spelling	oai:doaj.org-article:6668b00ffc3645e09f78470e071440592021-12-02T12:11:12ZPerformance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework10.1038/s41598-020-79778-x2045-2322https://doaj.org/article/6668b00ffc3645e09f78470e071440592021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79778-xhttps://doaj.org/toc/2045-2322Abstract Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.Philipp KirschnerWolfgang ArthoferStefanie PfeifenbergerEliška ZáveskáPeter SchönswetterThe STEPPE ConsortiumFlorian M. SteinerBirgit C. Schlick-SteinerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Philipp Kirschner Wolfgang Arthofer Stefanie Pfeifenberger Eliška Záveská Peter Schönswetter The STEPPE Consortium Florian M. Steiner Birgit C. Schlick-Steiner Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
description	Abstract Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
format	article
author	Philipp Kirschner Wolfgang Arthofer Stefanie Pfeifenberger Eliška Záveská Peter Schönswetter The STEPPE Consortium Florian M. Steiner Birgit C. Schlick-Steiner
author_facet	Philipp Kirschner Wolfgang Arthofer Stefanie Pfeifenberger Eliška Záveská Peter Schönswetter The STEPPE Consortium Florian M. Steiner Birgit C. Schlick-Steiner
author_sort	Philipp Kirschner
title	Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
title_short	Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
title_full	Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
title_fullStr	Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
title_full_unstemmed	Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
title_sort	performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/6668b00ffc3645e09f78470e07144059
work_keys_str_mv	AT philippkirschner performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT wolfgangarthofer performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT stefaniepfeifenberger performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT eliskazaveska performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT peterschonswetter performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT thesteppeconsortium performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT florianmsteiner performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework AT birgitcschlicksteiner performancecomparisonoftworeducedrepresentationbasedgenomewidemarkerdiscoverystrategiesinamultitaxonphylogeographicframework
_version_	1718394633362341888

Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Ejemplares similares