An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985939%3A_____%2F19%3A00510353" target="_blank" >RIV/67985939:_____/19:00510353 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/19:10407340

Výsledek na webu

<a href="http://hdl.handle.net/11104/0302385" target="_blank" >http://hdl.handle.net/11104/0302385</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/aps3.11295" target="_blank" >10.1002/aps3.11295</a>

Jazyk výsledku

angličtina

Název v původním jazyce

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Popis výsledku v původním jazyce

Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

Název v anglickém jazyce

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Popis výsledku anglicky

Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

<a href="/cs/project/GJ16-15134Y" target="_blank" >GJ16-15134Y: Nový pohled na starou problematiku: role celogenomových procesů v adaptivní radiaci rostlin studovaná pomocí moderních sekvenačních technik</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Applications in Plant Sciences

ISSN

2168-0450

e-ISSN

—

Svazek periodika

7

Číslo periodika v rámci svazku

10

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

27

Strana od-do

1-27

Kód UT WoS článku

000493059500001

EID výsledku v databázi Scopus

2-s2.0-85074167898